{ "cells": [ { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [], "source": [ "%matplotlib inline\n", "import pandas as pd\n", "import numpy as np\n", "import re\n", "import os\n", "import math\n", "from multiprocessing import Pool\n", "from tqdm import tqdm\n", "from scipy import stats\n", "## init\n", "mySpecie='Homo_sapiens'\n", "#prealigned_dir='/cellar/users/btsui/all_seq_snp/Homo_sapiens_all_merged_snp.TCGA.prealigned.pickle'\n", "targetted_align_dir='/cellar/users/btsui/all_seq_snp/Homo_sapiens_all_merged_snp.TCGA.pickle'\n", "manifest_dir='/cellar/users/btsui/Project/METAMAP/notebook/RapMapTest/XGS_WGS/./tcga_lgg_wgs_bams.df.wxs_rnaseq.pickle'\n", "\n", "targetted_df=pd.read_pickle(targetted_align_dir).loc[\"TCGA\"]" ] }, { "cell_type": "code", "execution_count": 3, "metadata": {}, "outputs": [], "source": [ "all_UUIDs=targetted_df.index.get_level_values('Run_digits').unique()" ] }, { "cell_type": "code", "execution_count": 4, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "n UUID: 1570\n" ] } ], "source": [ "#883, 1427\n", "print ('n UUID:',len(all_UUIDs))" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### annotate metadata" ] }, { "cell_type": "code", "execution_count": 5, "metadata": {}, "outputs": [], "source": [ "manifest_df=pd.read_pickle(manifest_dir)\n", "\n", "manifest_df['processed']=manifest_df.file_id.isin(all_UUIDs)\n", "\n", "uuid_barcode_mapDf=pd.read_csv('/cellar/users/andreabc/GDC_barcodes/uuid_barcode_map.txt',sep='\\t').set_index('file_id')\n", "\n", "manifest_df['sample_barcode']=uuid_barcode_mapDf.loc[manifest_df.file_id]['sample_barcode'].values\n", "\n", "m_data_category=manifest_df.data_category=='Raw Sequencing Data'\n", "m_experimental_strategy=manifest_df['experimental_strategy'].isin(['RNA-Seq','WXS'])\n", "\n", "manifest_df_sub=manifest_df[manifest_df['processed']&m_data_category&m_experimental_strategy]\n", "\n", "tmpVC=manifest_df_sub['sample_barcode'].value_counts()\n", "\n", "#identify data with both RNAseq and WXS\n", "with_both=tmpVC.index[tmpVC==2]\n", "\n", "manifest_df_w_RNA_WXS=manifest_df_sub[manifest_df_sub.sample_barcode.isin(with_both)]\n" ] }, { "cell_type": "code", "execution_count": 6, "metadata": {}, "outputs": [], "source": [] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### load in dbSNP vcf" ] }, { "cell_type": "code", "execution_count": 7, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/IPython/core/interactiveshell.py:2785: DtypeWarning: Columns (0) have mixed types. Specify dtype option on import or set low_memory=False.\n", " interactivity=interactivity, compiler=compiler, result=result)\n" ] } ], "source": [ "inVcfDir='/data/cellardata/users/btsui/dbsnp/Homo_sapiens/All_20170710.f1_byte2_not_00.vcf.gz' \n", "vcfDf=pd.read_csv(inVcfDir,sep='\\t',header=None)\n", "vcfDf.columns=['Chr','Pos','RsId','RefBase','AltBase','','','Annot']\n", "vcfDf['Chr']=vcfDf['Chr'].astype(np.str)" ] }, { "cell_type": "code", "execution_count": 8, "metadata": {}, "outputs": [], "source": [ "refI=vcfDf.drop_duplicates(['Chr','Pos','RefBase']).set_index(['Chr','Pos','RefBase']).index" ] }, { "cell_type": "code", "execution_count": 22, "metadata": {}, "outputs": [], "source": [ "\"\"\"for _,vcfDfRowS in vcfDf.iterrows():\n", " query_chromosome,qeury_corrdinate=vcfDfRowS['Chr'],vcfDfRowS['Pos']\n", " selectedBase=vcfDfRowS['AltBase']\n", " break\"\"\"\n", "\n", "#varscanVcfMerged=pd.read_pickle('/cellar/users/btsui/Project/METAMAP/notebook/RapMapTest/XGS_WGS/Data/TCGA_VCF.varscan_dr.pickle')" ] }, { "cell_type": "code", "execution_count": 44, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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ChrPosRsIdRefBaseAltBaseAnnot
1844058142877758rs75717953TC..RS=75717953;RSPOS=142877758;dbSNPBuildID=131;S...
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accessannotationscasesdata_categorydata_formatdata_typeexperimental_strategyfile_idfile_namefile_sizeplatformprocessedsample_barcode
546controlledNaN[{'project': {'project_id': 'TCGA-LGG'}, 'case...Raw Sequencing DataBAMAligned ReadsRNA-Seq1985b367-00c4-4c25-b049-5858e937cc6d948a7b5a-de83-41db-85f1-93a1a9b109ba_gdc_realn...3293981085IlluminaTrueTCGA-HT-A4DV-01A
1019controlledNaN[{'project': {'project_id': 'TCGA-LGG'}, 'case...Raw Sequencing DataBAMAligned ReadsRNA-Seqa7aff6a7-cea4-42e9-8d56-b211843a03028e4c32f5-1ed2-453b-b029-db7836249d3b_gdc_realn...4070637137IlluminaTrueTCGA-HT-A4DS-01A
860controlledNaN[{'project': {'project_id': 'TCGA-LGG'}, 'case...Raw Sequencing DataBAMAligned ReadsRNA-Seq4038984b-21d1-45d3-a5bb-208f9e71aa78b52aeb27-8d06-4a1c-b322-ee947261e95c_gdc_realn...4195199173IlluminaTrueTCGA-FG-A4MW-01A
791controlledNaN[{'project': {'project_id': 'TCGA-LGG'}, 'case...Raw Sequencing DataBAMAligned ReadsRNA-Seq7b17a5ef-c778-4753-8c30-427af9171f7aa9bfcb6f-ce2b-47e2-a2e2-dd777b6d1344_gdc_realn...4436516715IlluminaTrueTCGA-DB-A4XC-01A
1285controlledNaN[{'project': {'project_id': 'TCGA-LGG'}, 'case...Raw Sequencing DataBAMAligned ReadsRNA-Seq93e20db7-4892-4ef8-9331-ecd665e4cb9133262d51-82cb-4fe6-89d1-b7e1c4673896_gdc_realn...4501820893IlluminaTrueTCGA-FG-A4MX-01A
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" ], "text/plain": [ " access annotations \\\n", "546 controlled NaN \n", "1019 controlled NaN \n", "860 controlled NaN \n", "791 controlled NaN \n", "1285 controlled NaN \n", "\n", " cases data_category \\\n", "546 [{'project': {'project_id': 'TCGA-LGG'}, 'case... Raw Sequencing Data \n", "1019 [{'project': {'project_id': 'TCGA-LGG'}, 'case... Raw Sequencing Data \n", "860 [{'project': {'project_id': 'TCGA-LGG'}, 'case... Raw Sequencing Data \n", "791 [{'project': {'project_id': 'TCGA-LGG'}, 'case... Raw Sequencing Data \n", "1285 [{'project': {'project_id': 'TCGA-LGG'}, 'case... Raw Sequencing Data \n", "\n", " data_format data_type experimental_strategy \\\n", "546 BAM Aligned Reads RNA-Seq \n", "1019 BAM Aligned Reads RNA-Seq \n", "860 BAM Aligned Reads RNA-Seq \n", "791 BAM Aligned Reads RNA-Seq \n", "1285 BAM Aligned Reads RNA-Seq \n", "\n", " file_id \\\n", "546 1985b367-00c4-4c25-b049-5858e937cc6d \n", "1019 a7aff6a7-cea4-42e9-8d56-b211843a0302 \n", "860 4038984b-21d1-45d3-a5bb-208f9e71aa78 \n", "791 7b17a5ef-c778-4753-8c30-427af9171f7a \n", "1285 93e20db7-4892-4ef8-9331-ecd665e4cb91 \n", "\n", " file_name file_size platform \\\n", "546 948a7b5a-de83-41db-85f1-93a1a9b109ba_gdc_realn... 3293981085 Illumina \n", "1019 8e4c32f5-1ed2-453b-b029-db7836249d3b_gdc_realn... 4070637137 Illumina \n", "860 b52aeb27-8d06-4a1c-b322-ee947261e95c_gdc_realn... 4195199173 Illumina \n", "791 a9bfcb6f-ce2b-47e2-a2e2-dd777b6d1344_gdc_realn... 4436516715 Illumina \n", "1285 33262d51-82cb-4fe6-89d1-b7e1c4673896_gdc_realn... 4501820893 Illumina \n", "\n", " processed sample_barcode \n", "546 True TCGA-HT-A4DV-01A \n", "1019 True TCGA-HT-A4DS-01A \n", "860 True TCGA-FG-A4MW-01A \n", "791 True TCGA-DB-A4XC-01A \n", "1285 True TCGA-FG-A4MX-01A " ] }, "execution_count": 15, "metadata": {}, "output_type": "execute_result" } ], "source": [ "manifest_df_w_RNA_WXS.head()" ] }, { "cell_type": "code", "execution_count": 19, "metadata": {}, "outputs": [ { "data": { "text/plain": [ "Index(['TCGA-P5-A5EV-01A', 'TCGA-TQ-A7RI-01A', 'TCGA-HT-7478-01A',\n", " 'TCGA-QH-A6X8-01A', 'TCGA-HT-7472-01A', 'TCGA-HW-7495-01A',\n", " 'TCGA-DU-7007-01A', 'TCGA-QH-A6CU-01A', 'TCGA-DB-A64R-01A',\n", " 'TCGA-DU-A6S2-01A',\n", " ...\n", " 'TCGA-QH-A65Z-01A', 'TCGA-RY-A845-01A', 'TCGA-S9-A6U9-01A',\n", " 'TCGA-DH-A7UV-01A', 'TCGA-DU-6402-01A', 'TCGA-DU-6404-01A',\n", " 'TCGA-WH-A86K-01A', 'TCGA-DU-A5TP-01A', 'TCGA-HT-A61B-01A',\n", " 'TCGA-HT-7677-01A'],\n", " dtype='object', length=524)" ] }, "execution_count": 19, "metadata": {}, "output_type": "execute_result" } ], "source": [] }, { "cell_type": "code", "execution_count": 21, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ " 23%|██▎ | 119/524 [10:04<34:18, 5.08s/it]" ] }, { "ename": "KeyboardInterrupt", "evalue": "", "output_type": "error", "traceback": [ "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", "\u001b[0;31mKeyboardInterrupt\u001b[0m Traceback (most recent call last)", "\u001b[0;32m\u001b[0m in \u001b[0;36m\u001b[0;34m()\u001b[0m\n\u001b[1;32m 12\u001b[0m \u001b[0;31m### take only sites with one allele detected\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 13\u001b[0m \u001b[0mhomozygous_pos\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mwxsChrPosCountS\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mwxsChrPosCountS\u001b[0m\u001b[0;34m==\u001b[0m\u001b[0;36m1\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mindex\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 14\u001b[0;31m 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wxsTargettedDf=targetted_df.loc[wxsUUID].reset_index().set_index(['Chr','Pos'])\n", "\n", " wxsChrPosCountS=wxsTargettedDf.groupby(['Chr','Pos']).size()\n", " ### take only sites with one allele detected\n", " homozygous_pos=wxsChrPosCountS[wxsChrPosCountS==1].index\n", " m_homozygous=wxsTargettedDf.index.isin(homozygous_pos)\n", " wxsTargettedDf_homo=wxsTargettedDf[m_homozygous]\n", " wxsTargettedDf_homo=wxsTargettedDf_homo.reset_index().set_index(['Chr','Pos','base'])\n", "\n", " wxsTargettedDf_homo['is_ref_base']=wxsTargettedDf_homo.index.isin(refI)\n", "\n", " (~wxsTargettedDf_homo['is_ref_base']).mean()\n", " ### ignore the references\n", " homoGermlineVariantDf=wxsTargettedDf_homo[(~wxsTargettedDf_homo['is_ref_base'])&(wxsTargettedDf_homo['ReadDepth']>=2)&(wxsTargettedDf_homo['AverageBaseQuality']>=30)]\n", " \n", " ## check against RNAseq for the variants\n", " #For homozygous germ line variants, only the reference allele are supposed to be detected\n", "\n", " rnaTagettedDf=targetted_df.loc[rnaseqUUID]\n", " rnaTagettedDf=rnaTagettedDf[rnaTagettedDf['AverageBaseQuality']>=30]\n", "\n", " rnaseqSiteI=rnaTagettedDf.reset_index().set_index(['Chr','Pos']).index\n", " wxsHomoSiteI=homoGermlineVariantDf.reset_index().set_index(['Chr','Pos']).index\n", "\n", " interRd=np.intersect1d(wxsHomoSiteI[homoGermlineVariantDf['ReadDepth']>=10],rnaseqSiteI[rnaTagettedDf['ReadDepth']>=10])\n", " \n", " nsitesWithReads=len(interRd)\n", " #print (nsitesWithReads)\n", "\n", " homoGermlineVariantDf.head()\n", "\n", " tmpDf=rnaTagettedDf.unstack()['ReadDepth']\n", "\n", " rnaTagettedFractS=(tmpDf.T/tmpDf.sum(axis=1)).T.stack().to_frame('AllelicFract')\n", "\n", " #inter\n", "\n", " wgxGermlineVarM=rnaTagettedFractS.reset_index().set_index(['Chr','Pos','base']).index.isin(homoGermlineVariantDf.index)\n", " germLineDf=rnaTagettedFractS[wgxGermlineVarM]\n", " statDict[querySample]={'percentage_germline_var_with_1_AF':(germLineDf['AllelicFract']==1.0).mean(),\n", " 'nsites_overlap':nsitesWithReads,\n", " 'is_alt':(~wxsTargettedDf_homo['is_ref_base']).mean()}" ] }, { "cell_type": "code", "execution_count": 24, "metadata": {}, "outputs": [], "source": [ "statDf=pd.DataFrame(statDict).T" ] }, { "cell_type": "code", "execution_count": 32, "metadata": {}, "outputs": [], "source": [ "import seaborn as sns" ] }, { "cell_type": "code", "execution_count": 33, "metadata": {}, "outputs": [ { "data": { "text/plain": [ "" ] }, "execution_count": 33, "metadata": {}, "output_type": "execute_result" }, { "data": { "image/png": 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\n", 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" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "ax=statDf['percentage_germline_var_with_1_AF'].hist(normed=True)\n", "ax.grid(False)\n", "ax.set_xlabel('percentage_germline_var_with_1_AF')\n", "ax.set_ylabel('% of RNAseq samples')" ] }, { "cell_type": "code", "execution_count": 31, "metadata": {}, "outputs": [ { "data": { "text/plain": [ "is_alt 0.106553\n", "nsites_overlap 3515.250000\n", "percentage_germline_var_with_1_AF 0.955057\n", "Name: 0.025, dtype: float64" ] }, "execution_count": 31, "metadata": {}, "output_type": "execute_result" } ], "source": [ "statDf.quantile(axis=0,q=0.025)" ] }, { "cell_type": "code", "execution_count": 26, "metadata": {}, "outputs": [ { "data": { "text/plain": [ "is_alt 0.112343\n", "nsites_overlap 5827.000000\n", "percentage_germline_var_with_1_AF 0.971341\n", "dtype: float64" ] }, "execution_count": 26, "metadata": {}, "output_type": "execute_result" } ], "source": [ "statDf.median(axis=0)" ] }, { "cell_type": "code", "execution_count": 353, "metadata": {}, "outputs": [ { "data": { "text/plain": [ "0.987914744012305" ] }, "execution_count": 353, "metadata": {}, "output_type": "execute_result" } ], "source": [ "(germLineDf['AllelicFract']==1.0).mean()" ] }, { "cell_type": "code", "execution_count": 354, "metadata": {}, "outputs": [], "source": [ "rnaTargettedReI=rnaTagettedDf[rnaseqSiteI.isin(interRd)].reset_index().set_index(['Chr','Pos','base'])#[interRd]#" ] }, { "cell_type": "code", "execution_count": 314, "metadata": {}, "outputs": [], "source": [ "rnaTargettedReI['in_homo']=rnaTargettedReI.index.isin(homoGermlineVariantDf.index)" ] }, { "cell_type": "code", "execution_count": 315, "metadata": {}, "outputs": [ { "data": { "text/plain": [ "0.9769743920809124" ] }, "execution_count": 315, "metadata": {}, "output_type": "execute_result" } ], "source": [ "rnaTargettedReI.in_homo.mean()" ] }, { "cell_type": "code", "execution_count": 312, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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ReadDepthin_homo
ChrPosbase
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1046551G1.000000True
1049927G1.000000True
1338000C1.000000True
1338032G1.000000True
1338044G1.000000True
1338086A1.000000True
1338092A1.000000True
1338096C1.000000True
1338098G1.000000True
1338107C1.000000True
1398672C1.000000True
2306122G1.000000True
2406580C1.000000True
2408713C1.000000True
2408714A1.000000True
2408760G1.000000True
10375266A1.000000True
11792316A1.000000True
11796340C1.000000True
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11950377C1.000000True
11950455C1.000000True
11998841T1.000000True
12022869G1.000000True
15933236C1.000000True
16986614A1.000000True
16986848A1.000000True
16986885G1.000000True
16987159C0.014388False
...............
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154359619T1.000000True
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154379719A1.000000True
154380001T1.000000True
154380246A1.000000True
154380976T1.000000True
154414148A1.000000True
154420665C1.000000True
154420704C0.017241False
T0.982759True
154442419C0.002853False
T0.997147True
154532439G1.000000True
154533012C1.000000True
154546045C1.000000True
154556194C0.983051True
T0.016949False
154556237G1.000000True
154560549T1.000000True
154765467T1.000000True
154765524G1.000000True
154765948T1.000000True
155090807C1.000000True
155260815T1.000000True
155506930G1.000000True
\n", "

4647 rows × 2 columns

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featuresReadDepthAverageBaseQualityis_ref_base
ChrPosbase
11013541C3430False
1041950C3829False
1042190A1831False
1043223C1031False
1045707G4327False
1046551G3328False
1047561C6231False
1049927G5431False
1051820T2832False
1086035G2731False
1232684G2932False
1338000C2632False
1338032G2931False
1338044G3131False
1338086A1829False
1338092A1631False
1338096C1630False
1338098G1730False
1338107C1625False
1398672C5732False
1955672G6732False
2024923A3333False
2229045G2327False
2306122G1432False
2406580C4432False
2408713C1932False
2408714A2132False
2408760G4634False
3402939T7329False
3403006G2531False
..................
X154966119T6031False
154966498G3734False
154966616C6033False
154966617T5833False
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154996995T14331False
154999531T9831False
154999543C10733False
155090807C1332False
155260815T14131False
155506930G7534False
Y5057021G4833False
5207530G4433False
5207641C10432False
5207717C4532False
10175852C2031False
16618833C5729False
16618838C5634False
26329144A1931False
26332935C11832False
26333008A5331False
26333079G2033False
26333764G3434False
26337383A3431False
26401079A1232False
26420452C2533False
26420477G2927False
26557077T8833False
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15630 rows × 3 columns

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" ], "text/plain": [ "features ReadDepth AverageBaseQuality is_ref_base\n", "Chr Pos base \n", "1 1013541 C 34 30 False\n", " 1041950 C 38 29 False\n", " 1042190 A 18 31 False\n", " 1043223 C 10 31 False\n", " 1045707 G 43 27 False\n", " 1046551 G 33 28 False\n", " 1047561 C 62 31 False\n", " 1049927 G 54 31 False\n", " 1051820 T 28 32 False\n", " 1086035 G 27 31 False\n", " 1232684 G 29 32 False\n", " 1338000 C 26 32 False\n", " 1338032 G 29 31 False\n", " 1338044 G 31 31 False\n", " 1338086 A 18 29 False\n", " 1338092 A 16 31 False\n", " 1338096 C 16 30 False\n", " 1338098 G 17 30 False\n", " 1338107 C 16 25 False\n", " 1398672 C 57 32 False\n", " 1955672 G 67 32 False\n", " 2024923 A 33 33 False\n", " 2229045 G 23 27 False\n", " 2306122 G 14 32 False\n", " 2406580 C 44 32 False\n", " 2408713 C 19 32 False\n", " 2408714 A 21 32 False\n", " 2408760 G 46 34 False\n", " 3402939 T 73 29 False\n", " 3403006 G 25 31 False\n", "... ... ... ...\n", "X 154966119 T 60 31 False\n", " 154966498 G 37 34 False\n", " 154966616 C 60 33 False\n", " 154966617 T 58 33 False\n", " 154969396 G 82 34 False\n", " 154969432 G 116 29 False\n", " 154984784 T 89 31 False\n", " 154996995 T 143 31 False\n", " 154999531 T 98 31 False\n", " 154999543 C 107 33 False\n", " 155090807 C 13 32 False\n", " 155260815 T 141 31 False\n", " 155506930 G 75 34 False\n", "Y 5057021 G 48 33 False\n", " 5207530 G 44 33 False\n", " 5207641 C 104 32 False\n", " 5207717 C 45 32 False\n", " 10175852 C 20 31 False\n", " 16618833 C 57 29 False\n", " 16618838 C 56 34 False\n", " 26329144 A 19 31 False\n", " 26332935 C 118 32 False\n", " 26333008 A 53 31 False\n", " 26333079 G 20 33 False\n", " 26333764 G 34 34 False\n", " 26337383 A 34 31 False\n", " 26401079 A 12 32 False\n", " 26420452 C 25 33 False\n", " 26420477 G 29 27 False\n", " 26557077 T 88 33 False\n", "\n", "[15630 rows x 3 columns]" ] }, "execution_count": 233, "metadata": {}, "output_type": "execute_result" } ], "source": [] }, { "cell_type": "code", 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1049927 G 0.988764\n", " 1051820 T 1.000000\n", " 1338000 C 1.000000\n", " 1338032 G 1.000000\n", " 1338044 G 1.000000\n", " 1338086 A 1.000000\n", " 1338092 A 1.000000\n", " 1338096 C 1.000000\n", " 1338098 G 1.000000\n", " 1338107 C 1.000000\n", " 1398672 C 1.000000\n", " 2229045 G 1.000000\n", " 2306122 G 1.000000\n", " 2406580 C 1.000000\n", " 2408713 C 1.000000\n", " 2408714 A 1.000000\n", " 2408760 G 1.000000\n", " 3411655 C 1.000000\n", " 3478076 G 1.000000\n", " 3478110 C 1.000000\n", " 5877256 C 1.000000\n", " 5877331 T 1.000000\n", " 7640514 T 1.000000\n", " 7663384 C 1.000000\n", " 7663428 C 1.000000\n", " 7809988 C 1.000000\n", " 7827433 C 1.000000\n", " ... \n", "X 154420878 G 1.000000\n", " 154442419 T 0.995726\n", " 154532439 G 1.000000\n", " 154533012 C 1.000000\n", " 154546045 C 1.000000\n", " 154556194 C 0.983051\n", " 154556237 G 1.000000\n", " 154560549 T 1.000000\n", " 154563953 T 1.000000\n", " 154765467 T 1.000000\n", " 154765524 G 1.000000\n", " 154765948 T 1.000000\n", " 154776813 C 1.000000\n", " 154837734 C 1.000000\n", " 154860536 C 1.000000\n", " 154861741 T 1.000000\n", " 154863191 G 1.000000\n", " 154896092 G 1.000000\n", " 154929458 A 1.000000\n", " 154929489 T 1.000000\n", " 154930240 C 1.000000\n", " 155090807 C 1.000000\n", " 155260815 T 1.000000\n", " 155506930 G 1.000000\n", "Y 5207641 C 1.000000\n", " 16618833 C 1.000000\n", " 16618838 C 1.000000\n", " 26332935 C 1.000000\n", " 26420452 C 1.000000\n", " 26420477 G 1.000000\n", "Length: 9191, dtype: float64" ] }, "execution_count": 232, "metadata": {}, "output_type": "execute_result" } ], "source": [ "rnaSeqS" ] }, { "cell_type": "code", "execution_count": 207, "metadata": {}, "outputs": [], "source": [ "m=rnaSeqS.index.isin(homoGermlineVariantDf.index)\n", "allelicFractionInGermlineS=rnaSeqS[m]" ] }, { "cell_type": "code", "execution_count": 220, "metadata": {}, "outputs": [ { "data": { "text/plain": [ "0.017158015785897235" ] }, "execution_count": 220, "metadata": {}, "output_type": "execute_result" } ], "source": [ "m.mean()" ] }, { "cell_type": "code", "execution_count": 216, "metadata": {}, "outputs": [ { "data": { "text/plain": [ "9191" ] }, "execution_count": 216, "metadata": {}, "output_type": "execute_result" } ], "source": [ "len(allelicFractionInGermlineS)" ] }, { "cell_type": "code", "execution_count": 210, "metadata": {}, "outputs": [ { "data": { "text/plain": [ "9191" ] }, "execution_count": 210, "metadata": {}, "output_type": "execute_result" } ], "source": [ "len(allelicFractionInGermlineS)" ] }, { "cell_type": "code", "execution_count": 213, "metadata": {}, "outputs": [], "source": [ "#allelicFractionInGermlineS[allelicFractionInGermlineS==0]" ] }, { "cell_type": "code", "execution_count": 212, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/matplotlib/axes/_axes.py:6462: UserWarning: The 'normed' kwarg is deprecated, and has been replaced by the 'density' kwarg.\n", " warnings.warn(\"The 'normed' kwarg is deprecated, and has been \"\n" ] }, { "data": { "text/plain": [ "Text(0,0.5,'% of germline variants')" ] }, "execution_count": 212, "metadata": {}, "output_type": "execute_result" }, { "data": { "image/png": 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\n", "text/plain": [ "
" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "ax=allelicFractionInGermlineS[allelicFractionInGermlineS>=0].hist(bins=10,normed=True)\n", "ax.set_xlabel('Allelic fraction')\n", "ax.set_ylabel('% of germline variants')\n" ] }, { "cell_type": "code", "execution_count": 158, "metadata": { "scrolled": true }, "outputs": [ { "data": { "text/plain": [ "" ] }, "execution_count": 158, "metadata": {}, "output_type": "execute_result" }, { "data": { "image/png": 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zAc9vyy/gkPcRrTRV9Xlg71N02QR8osZuA45JcvxiHX+lB8BsHy2x9nB9quoAsA940URmtzSG1DzTVsavIFayOWtO8irgxKr63CQntoSG/JxfBrwsyT8nuS3JxonNbmkMqfmPgLcm2cP4acJ3TmZqy2a+/9/nZeKPgS6yOT9aYmCflWRwPUneCkwBv7SkM1p6T1lzkmcAlwLnT2pCEzDk57yK8WWgacZnef+Y5JVV9cQSz22pDKn5LcAVVfVnSV4DfLLV/H9LP71lsaR/v1b6GcCcHy0xs0+SVYxPG5/qlOvpbkjNJHkj8IfA2VX13QnNbanMVfPzgFcCoyRfY3ytdOcKvxE89Hf7uqr636p6ELiPcSCsVENq3gpcA1BV/wI8m/HnBP2kGvT//Uit9AAY8tESO4Etbflc4JZqd1dWqDlrbpdD/pLxH/+Vfl0Y5qi5qvZV1XFVta6q1jG+73F2Vd2+PNNdFEN+t/+O8Q1/khzH+JLQAxOd5eIaUvNDwAaAJC9nHADfnOgsJ2sn8Lb2NNDpwL6qenSxdr6iLwHVYT5aIsl7gduraidwGePTxN2MX/lvXr4ZL9zAmv8EeC7wmXa/+6GqOnvZJr1AA2v+iTKw5huBM5LcA3wf+N2q+q/lm/XCDKz5QuCvkryb8aWQ81fyC7okn2Z8Ce+4dl/jIuCZAFX1Mcb3Oc4CdgNPAm9f1OOv4H87SdICrPRLQJKkI2QASFKnDABJ6pQBIEmdMgAkqVMGgCR1ygCQpE4ZAJLUqf8HcgnxFJ0AKSQAAAAASUVORK5CYII=\n", "text/plain": [ "
" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "\n", "rnaSeqS[rnaSeqS.index.isin(homoGermlineVariantDf.index)].hist()" ] }, { "cell_type": "code", "execution_count": 159, "metadata": {}, "outputs": [ { "data": { "text/plain": [ "0.5867562380038388" ] }, "execution_count": 159, "metadata": {}, "output_type": "execute_result" } ], "source": [ "germlineVariantDf.index.isin(rnaTagettedDf.index).mean()" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "# scratch" ] }, { "cell_type": "code", "execution_count": 33, "metadata": {}, "outputs": [], "source": [ "#topTcgaVcfDf_inTargeted.head()" ] }, { "cell_type": "code", "execution_count": 34, "metadata": {}, "outputs": [], "source": [ "threshold=2" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "#### extract all the germ line variants, " ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "[{'auprc': 0.9982105610204264, 'vcfIndex': ('2', 208248388), 'rocauc': 0.9842904603701946, 'rnaseq_rd': 133.82251908396947, 'rnaseq_n': 519}]\n", "1\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "[{'auprc': 0.5436157339090322, 'vcfIndex': ('17', 7673803), 'rocauc': 0.9452658347625525, 'rnaseq_rd': 122.07633587786259, 'rnaseq_n': 520}]\n", "2\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "failed\n", "failed\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "[{'auprc': 0.8651493930905695, 'vcfIndex': ('2', 208248389), 'rocauc': 0.8964102564102564, 'rnaseq_rd': 133.3759541984733, 'rnaseq_n': 519}]\n", "3\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "[{'auprc': 0.9915456162454604, 'vcfIndex': ('14', 32092134), 'rocauc': 0.5077669902912622, 'rnaseq_rd': 38.31297709923664, 'rnaseq_n': 457}]\n", "4\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "failed\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "[{'auprc': 0.9517857142857143, 'vcfIndex': ('2', 208248389), 'rocauc': 0.9577020202020201, 'rnaseq_rd': 133.3759541984733, 'rnaseq_n': 519}]\n", "5\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "[{'auprc': 1.0, 'vcfIndex': ('15', 90088606), 'rocauc': 1.0, 'rnaseq_rd': 353.8416030534351, 'rnaseq_n': 524}]\n", "6\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "[{'auprc': 0.954090909090909, 'vcfIndex': ('17', 7673802), 'rocauc': 0.9488888888888888, 'rnaseq_rd': 121.37284894837477, 'rnaseq_n': 520}]\n", "7\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "[{'auprc': 0.7384169884169884, 'vcfIndex': ('8', 142877758), 'rocauc': 0.5, 'rnaseq_rd': 0.0019305019305019305, 'rnaseq_n': 0}]\n", "8\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "[{'auprc': 0.9895369944981679, 'vcfIndex': ('X', 24789042), 'rocauc': 0.5035885167464115, 'rnaseq_rd': 5.2629482071713145, 'rnaseq_n': 91}]\n", "9\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "failed\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "[{'auprc': 0.9999400689281579, 'vcfIndex': ('1', 109690516), 'rocauc': 0.9965412883700822, 'rnaseq_rd': 210.7767175572519, 'rnaseq_n': 513}]\n", "10\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "[{'auprc': 0.9751543209876543, 'vcfIndex': ('17', 7674872), 'rocauc': 0.9993704752911552, 'rnaseq_rd': 59.13549618320611, 'rnaseq_n': 496}]\n", "11\n", "failed\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "[{'auprc': 0.6849247001118479, 'vcfIndex': ('6', 29944050), 'rocauc': 0.6133071391504189, 'rnaseq_rd': 16.24236641221374, 'rnaseq_n': 286}]\n", "12\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "[{'auprc': 1.0, 'vcfIndex': ('2', 208248389), 'rocauc': 1.0, 'rnaseq_rd': 133.3759541984733, 'rnaseq_n': 519}]\n", "13\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "failed\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "failed\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "[{'auprc': 0.998226347522553, 'vcfIndex': ('X', 24788994), 'rocauc': 0.6949317738791423, 'rnaseq_rd': 1291.3740458015268, 'rnaseq_n': 524}]\n", "14\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "[{'auprc': 0.9941271648588722, 'vcfIndex': ('12', 6018369), 'rocauc': 0.6216216216216216, 'rnaseq_rd': 36.32053742802303, 'rnaseq_n': 431}]\n", "15\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "failed\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "failed\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "[{'auprc': 0.8950736763236764, 'vcfIndex': ('17', 7674220), 'rocauc': 0.9293664383561644, 'rnaseq_rd': 124.63671128107075, 'rnaseq_n': 520}]\n", "16\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "[{'auprc': 0.8500000000000001, 'vcfIndex': ('17', 7675076), 'rocauc': 0.9983935742971888, 'rnaseq_rd': 91.69083969465649, 'rnaseq_n': 510}]\n", "17\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "[{'auprc': 0.7798582995951417, 'vcfIndex': ('17', 7675088), 'rocauc': 0.7655677655677655, 'rnaseq_rd': 107.20537428023033, 'rnaseq_n': 509}]\n", "18\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "failed\n", "failed\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "failed\n", "failed\n", "failed\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "[{'auprc': 0.9242947346041334, 'vcfIndex': ('12', 6018901), 'rocauc': 0.6154363110008272, 'rnaseq_rd': 79.05152671755725, 'rnaseq_n': 502}]\n", "19\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "[{'auprc': 0.967687875497635, 'vcfIndex': ('6', 31271836), 'rocauc': 0.6717948717948719, 'rnaseq_rd': 950.9332061068702, 'rnaseq_n': 524}]\n", "20\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "[{'auprc': 0.5249729346906801, 'vcfIndex': ('6', 31356729), 'rocauc': 0.4567348881485007, 'rnaseq_rd': 1370.7922330097088, 'rnaseq_n': 502}]\n", "21\n", "failed\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "[{'auprc': 0.9664750957854407, 'vcfIndex': ('7', 117548682), 'rocauc': 0.5, 'rnaseq_rd': 0.39272030651340994, 'rnaseq_n': 1}]\n", "22\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "[{'auprc': 0.8435959942590133, 'vcfIndex': ('6', 29943406), 'rocauc': 0.4709963985594237, 'rnaseq_rd': 2902.0687022900765, 'rnaseq_n': 522}]\n", "23\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "[{'auprc': 0.6240315082644627, 'vcfIndex': ('6', 29943422), 'rocauc': 0.5176321912862072, 'rnaseq_rd': 2319.403474903475, 'rnaseq_n': 480}]\n", "24\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "failed\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "failed\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "failed\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/sklearn/metrics/ranking.py:444: RuntimeWarning: invalid value encountered in true_divide\n", " recall = tps / tps[-1]\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "failed\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "failed\n", "failed\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/sklearn/metrics/ranking.py:444: RuntimeWarning: invalid value encountered in true_divide\n", " recall = tps / tps[-1]\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "failed\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/sklearn/metrics/ranking.py:444: RuntimeWarning: invalid value encountered in true_divide\n", " recall = tps / tps[-1]\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "failed\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "failed\n", "failed\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "[{'auprc': 0.9999999999999998, 'vcfIndex': ('17', 7674221), 'rocauc': 1.0, 'rnaseq_rd': 123.95602294455067, 'rnaseq_n': 520}]\n", "25\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "failed\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "[{'auprc': 0.9769153916419274, 'vcfIndex': ('7', 142750675), 'rocauc': 0.49849488260084285, 'rnaseq_rd': 0.3199152542372881, 'rnaseq_n': 3}]\n", "26\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/sklearn/metrics/ranking.py:444: RuntimeWarning: invalid value encountered in true_divide\n", " recall = tps / tps[-1]\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "failed\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/sklearn/metrics/ranking.py:444: RuntimeWarning: invalid value encountered in true_divide\n", " recall = tps / tps[-1]\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "failed\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "[{'auprc': 0.8815028901734103, 'vcfIndex': ('7', 152238825), 'rocauc': 0.5, 'rnaseq_rd': 9.790076335877863, 'rnaseq_n': 212}]\n", "27\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "[{'auprc': 0.7770187787215652, 'vcfIndex': ('17', 7673776), 'rocauc': 0.8756735950731331, 'rnaseq_rd': 121.84351145038168, 'rnaseq_n': 518}]\n", "28\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "[{'auprc': 0.5016891891891891, 'vcfIndex': ('9', 128257486), 'rocauc': 0.5, 'rnaseq_rd': 84.02579365079364, 'rnaseq_n': 472}]\n", "29\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "[{'auprc': 0.9621421257423716, 'vcfIndex': ('7', 142750600), 'rocauc': 0.5010526315789474, 'rnaseq_rd': 0.21595330739299612, 'rnaseq_n': 4}]\n", "30\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "[{'auprc': 0.11665167191482981, 'vcfIndex': ('7', 55165350), 'rocauc': 0.6013007054673721, 'rnaseq_rd': 300.21946564885496, 'rnaseq_n': 481}]\n", "31\n", "failed\n", "failed\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "failed\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "[{'auprc': 0.9994991036591797, 'vcfIndex': ('12', 2685853), 'rocauc': 0.7816091954022988, 'rnaseq_rd': 2.092741935483871, 'rnaseq_n': 8}]\n", "32\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/sklearn/metrics/ranking.py:444: RuntimeWarning: invalid value encountered in true_divide\n", " recall = tps / tps[-1]\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "failed\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "[{'auprc': 0.9612392525801189, 'vcfIndex': ('4', 144120554), 'rocauc': 0.4796998031496063, 'rnaseq_rd': 0.49236641221374045, 'rnaseq_n': 3}]\n", "33\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "failed\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/sklearn/metrics/ranking.py:444: RuntimeWarning: invalid value encountered in true_divide\n", " recall = tps / tps[-1]\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "failed\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "[{'auprc': 0.8670477230214318, 'vcfIndex': ('6', 29944118), 'rocauc': 0.6404452281243111, 'rnaseq_rd': 18.980582524271846, 'rnaseq_n': 315}]\n", "34\n", "failed\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "[{'auprc': 0.8319444444444444, 'vcfIndex': ('17', 7674230), 'rocauc': 0.8713235294117647, 'rnaseq_rd': 120.80534351145039, 'rnaseq_n': 519}]\n", "35\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "[{'auprc': 0.7957251082251082, 'vcfIndex': ('17', 7674945), 'rocauc': 0.869140625, 'rnaseq_rd': 99.9675572519084, 'rnaseq_n': 513}]\n", "36\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "failed\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "failed\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "[{'auprc': 0.9917339294729354, 'vcfIndex': ('19', 14766987), 'rocauc': 0.5071428571428571, 'rnaseq_rd': 1.315487571701721, 'rnaseq_n': 9}]\n", "37\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "failed\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "failed\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "[{'auprc': 0.718190399137001, 'vcfIndex': ('7', 55154129), 'rocauc': 0.8454455445544554, 'rnaseq_rd': 182.2767175572519, 'rnaseq_n': 464}]\n", "38\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "[{'auprc': 0.9565217391304348, 'vcfIndex': ('7', 127611678), 'rocauc': 0.5, 'rnaseq_rd': 0.06451612903225806, 'rnaseq_n': 0}]\n", "39\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/sklearn/metrics/ranking.py:444: RuntimeWarning: invalid value encountered in true_divide\n", " recall = tps / tps[-1]\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "failed\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "[{'auprc': 0.9811409712399812, 'vcfIndex': ('1', 235775088), 'rocauc': 0.504950495049505, 'rnaseq_rd': 0.0136986301369863, 'rnaseq_n': 0}]\n", "40\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "[{'auprc': 0.9224825164827356, 'vcfIndex': ('1', 173828313), 'rocauc': 0.501444707118466, 'rnaseq_rd': 2.292089249492901, 'rnaseq_n': 1}]\n", "41\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "failed\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "failed\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "[{'auprc': 0.9913282738681911, 'vcfIndex': ('2', 166281810), 'rocauc': 0.5231741573033708, 'rnaseq_rd': 1.3317073170731708, 'rnaseq_n': 15}]\n", "42\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/sklearn/metrics/ranking.py:444: RuntimeWarning: invalid value encountered in true_divide\n", " recall = tps / tps[-1]\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "failed\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "failed\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/sklearn/metrics/ranking.py:444: RuntimeWarning: invalid value encountered in true_divide\n", " recall = tps / tps[-1]\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "failed\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/sklearn/metrics/ranking.py:444: RuntimeWarning: invalid value encountered in true_divide\n", " recall = tps / tps[-1]\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "failed\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "failed\n", "failed\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "failed\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "failed\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "[{'auprc': 0.9444444444444444, 'vcfIndex': ('6', 32664778), 'rocauc': 0.5, 'rnaseq_rd': 2.370212765957447, 'rnaseq_n': 8}]\n", "43\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "failed\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "[{'auprc': 0.07298916724566964, 'vcfIndex': ('6', 31270232), 'rocauc': 0.5693114455084359, 'rnaseq_rd': 747.1783567134269, 'rnaseq_n': 401}]\n", "44\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "[{'auprc': 0.8904019236433559, 'vcfIndex': ('12', 52897420), 'rocauc': 0.5084404879657105, 'rnaseq_rd': 7.585603112840467, 'rnaseq_n': 71}]\n", "45\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "[{'auprc': 0.559769267265185, 'vcfIndex': ('6', 29942825), 'rocauc': 0.797976477463657, 'rnaseq_rd': 2793.31106870229, 'rnaseq_n': 524}]\n", "46\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "[{'auprc': 0.46834657753136016, 'vcfIndex': ('6', 29942845), 'rocauc': 0.4998989898989899, 'rnaseq_rd': 2905.9483747609943, 'rnaseq_n': 517}]\n", "47\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "[{'auprc': 0.9229132597203707, 'vcfIndex': ('6', 29944102), 'rocauc': 0.7980787271567413, 'rnaseq_rd': 21.58206106870229, 'rnaseq_n': 368}]\n", "48\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "[{'auprc': 0.8023328381245963, 'vcfIndex': ('6', 29944103), 'rocauc': 0.7773660377358491, 'rnaseq_rd': 21.608778625954198, 'rnaseq_n': 371}]\n", "49\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "[{'auprc': 0.9422616789380488, 'vcfIndex': ('6', 29944168), 'rocauc': 0.9607098982098983, 'rnaseq_rd': 4361.543893129771, 'rnaseq_n': 524}]\n", "50\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "[{'auprc': 0.5614637623652268, 'vcfIndex': ('12', 6018910), 'rocauc': 0.5450518969219758, 'rnaseq_rd': 73.97137404580153, 'rnaseq_n': 500}]\n", "51\n", "failed\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "failed\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "[{'auprc': 0.9961163900517636, 'vcfIndex': ('5', 236441), 'rocauc': 0.5004950495049505, 'rnaseq_rd': 189.5229007633588, 'rnaseq_n': 524}]\n", "52\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "[{'auprc': 0.7945205479452055, 'vcfIndex': ('3', 10064460), 'rocauc': 0.5, 'rnaseq_rd': 0.26705653021442494, 'rnaseq_n': 0}]\n", "53\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "failed\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "[{'auprc': 0.5047709923664122, 'vcfIndex': ('3', 179199690), 'rocauc': 0.5, 'rnaseq_rd': 10.774809160305344, 'rnaseq_n': 237}]\n", "54\n", "failed\n", "failed\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/sklearn/metrics/ranking.py:444: RuntimeWarning: invalid value encountered in true_divide\n", " recall = tps / tps[-1]\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "failed\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "failed\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "failed\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "failed\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "failed\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "[{'auprc': 0.8408395548245163, 'vcfIndex': ('6', 32661364), 'rocauc': 0.6422820109976433, 'rnaseq_rd': 113.46332046332046, 'rnaseq_n': 358}]\n", "55\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "[{'auprc': 0.9645215692947171, 'vcfIndex': ('6', 32661416), 'rocauc': 0.6010173721086477, 'rnaseq_rd': 214.6240458015267, 'rnaseq_n': 489}]\n", "56\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "[{'auprc': 0.035856045886774615, 'vcfIndex': ('22', 42127537), 'rocauc': 0.4298987568883762, 'rnaseq_rd': 17.948374760994263, 'rnaseq_n': 355}]\n", "57\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "[{'auprc': 0.9957796476538225, 'vcfIndex': ('6', 32661360), 'rocauc': 0.4311175337186898, 'rnaseq_rd': 97.21606118546845, 'rnaseq_n': 337}]\n", "58\n", "failed\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "[{'auprc': 0.9604493382073076, 'vcfIndex': ('6', 29943620), 'rocauc': 0.546979136482179, 'rnaseq_rd': 12.659655831739961, 'rnaseq_n': 238}]\n", "59\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "failed\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "[{'auprc': 0.7750889986870693, 'vcfIndex': ('6', 29944059), 'rocauc': 0.6722366428725935, 'rnaseq_rd': 17.18320610687023, 'rnaseq_n': 315}]\n", "60\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "[{'auprc': 0.9842224503338726, 'vcfIndex': ('6', 29944067), 'rocauc': 0.8036034099863886, 'rnaseq_rd': 16.535372848948374, 'rnaseq_n': 315}]\n", "61\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "failed\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "failed\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "failed\n" ] } ], "source": [ "#threshold=2\n", "\n", "#selectedBase='T'\n", "#query_chromosome, qeury_corrdinate='2',208248388\n", "failedS_L=[]\n", "roc_auc_l=[]\n", "m_chr=targetted_df.index.get_level_values('Chr')==query_chromosome\n", "Pos_array=targetted_df.index.get_level_values('Pos')\n", "successCount=0\n", "for vcfIndex,vcfDfRowS in topTcgaVcfDf_inTargeted.iterrows():\n", " try:\n", " query_chromosome,qeury_corrdinate=vcfDfRowS['CHROM'].replace('chr',''),vcfDfRowS['POS']\n", " selectedBase=vcfDfRowS['ALT']\n", "\n", " window_size=0\n", " \n", " m_pos=(Pos_array>=(qeury_corrdinate-window_size))&(Pos_array<=(qeury_corrdinate+window_size))\n", " if m_pos.sum()<10:\n", " print ('failed')\n", " continue\n", " m_qual=targetted_df['AverageBaseQuality']>=30\n", " #if m_pos.sum()>=0:\n", " targetted_df_sub=targetted_df[m_pos&m_qual]\n", "\n", " index_metaDf=targetted_df_sub.index.to_frame()\n", "\n", " index_metaDf['sample_barcode']=manifest_df_w_RNA_WXS.set_index('file_id').loc[index_metaDf['Run_digits']]['sample_barcode'].values\n", "\n", " multI=index_metaDf.set_index(['sample_barcode','Run_digits','Chr','Pos','base']).index\n", " targetted_df_sub.index=multI\n", "\n", "\n", " rnaseq_uuids=manifest_df_w_RNA_WXS[manifest_df_w_RNA_WXS['experimental_strategy']=='RNA-Seq']['file_id'].unique()\n", " m_uuid=targetted_df_sub.index.get_level_values('Run_digits').isin(rnaseq_uuids)\n", " rnaseq_df=targetted_df_sub[m_uuid]\n", "\n", " groupings_L=['sample_barcode','Chr','Pos','base']\n", "\n", " rnaseq_df=rnaseq_df.groupby(groupings_L).first()\n", "\n", " wxs_uuids=manifest_df_w_RNA_WXS[manifest_df_w_RNA_WXS['experimental_strategy']=='WXS']['file_id'].unique()\n", " m_uuid=targetted_df_sub.index.get_level_values('Run_digits').isin(wxs_uuids)\n", " wxs_df=targetted_df_sub[m_uuid]\n", "\n", " wxs_df=wxs_df.groupby(groupings_L).first()\n", "\n", " mergedDf=pd.concat([ rnaseq_df,wxs_df],axis=1,keys=['rna-seq','wxs'])\n", "\n", " mergedDf['wxs']['ReadDepth']=mergedDf['wxs']['ReadDepth'].fillna(0)\n", "\n", " #mergedDf\n", "\n", " #for the whole \n", "\n", " from sklearn import metrics\n", "\n", " #### get the homozygous\n", "\n", " wxsWithDataDf=mergedDf#[mergedDf['wxs']['ReadDepth']>=threshold]\n", "\n", " sampleRdS=wxsWithDataDf['wxs'].groupby('sample_barcode')['ReadDepth'].sum()\n", " sampleRdS_rnaseq=wxsWithDataDf['rna-seq'].groupby('sample_barcode')['ReadDepth'].sum()\n", " \n", " xwsSamplesWithCoverage=sampleRdS.index[sampleRdS>=threshold]\n", "\n", " m_base=wxsWithDataDf.index.get_level_values('base')==selectedBase\n", "\n", " m_wxs_coverage=wxsWithDataDf.index.get_level_values('sample_barcode').isin(xwsSamplesWithCoverage)\n", "\n", " m_valid_all=mergedDf.notnull().all(axis=1)\n", "\n", " wxsWithDataDf_base=wxsWithDataDf[m_base&m_wxs_coverage]\n", " wxsWithDataDf_base['rna-seq']=wxsWithDataDf_base['rna-seq'].fillna(0)\n", " y_true=wxsWithDataDf_base['wxs']['ReadDepth']>=threshold\n", " \n", " precision,recall,_=metrics.precision_recall_curve(y_true,\n", " wxsWithDataDf_base['rna-seq']['ReadDepth'].fillna(0))\n", " roc_auc=metrics.roc_auc_score(y_true,\n", " wxsWithDataDf_base['rna-seq']['ReadDepth'].fillna(0))\n", " auprc=metrics.auc(recall,precision)\n", " #print (auprc,wxsWithDataDf_base['rna-seq']['ReadDepth'].fillna(0).mean())\n", " myResultL=[{'auprc':auprc,'vcfIndex':vcfIndex,\"rocauc\":roc_auc,\n", " 'rnaseq_rd':sampleRdS_rnaseq.mean(),\n", " 'rnaseq_n':((sampleRdS_rnaseq>=10).sum())}]\n", "\n", " roc_auc_l+= myResultL \n", " print (myResultL)\n", " successCount+=1\n", " print (successCount)\n", " except ValueError:#ValueError\n", " failedS_L.append(vcfDfRowS)\n", " print ('failed')\n", "#group=wxsWithDataDf.groupby('base')\n", "\n", "#for base, df in group:\n", "# break" ] }, { "cell_type": "code", "execution_count": 193, "metadata": { "scrolled": true }, "outputs": [], "source": [ "praucDf=pd.DataFrame(roc_auc_l).dropna().head(n=100)#.to_frame('prauc')" ] }, { "cell_type": "code", "execution_count": 196, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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auprcrnaseq_nrnaseq_rdrocaucvcfIndex
00.998211519133.8225190.984290(2, 208248388)
10.543616520122.0763360.945266(17, 7673803)
20.865149519133.3759540.896410(2, 208248389)
30.99154645738.3129770.507767(14, 32092134)
40.951786519133.3759540.957702(2, 208248389)
51.000000524353.8416031.000000(15, 90088606)
60.954091520121.3728490.948889(17, 7673802)
70.73841700.0019310.500000(8, 142877758)
80.989537915.2629480.503589(X, 24789042)
90.999940513210.7767180.996541(1, 109690516)
100.97515449659.1354960.999370(17, 7674872)
110.68492528616.2423660.613307(6, 29944050)
121.000000519133.3759541.000000(2, 208248389)
130.9982265241291.3740460.694932(X, 24788994)
140.99412743136.3205370.621622(12, 6018369)
150.895074520124.6367110.929366(17, 7674220)
160.85000051091.6908400.998394(17, 7675076)
170.779858509107.2053740.765568(17, 7675088)
180.92429550279.0515270.615436(12, 6018901)
190.967688524950.9332060.671795(6, 31271836)
200.5249735021370.7922330.456735(6, 31356729)
210.96647510.3927200.500000(7, 117548682)
220.8435965222902.0687020.470996(6, 29943406)
230.6240324802319.4034750.517632(6, 29943422)
241.000000520123.9560231.000000(17, 7674221)
250.97691530.3199150.498495(7, 142750675)
260.8815032129.7900760.500000(7, 152238825)
270.777019518121.8435110.875674(17, 7673776)
280.50168947284.0257940.500000(9, 128257486)
290.96214240.2159530.501053(7, 142750600)
..................
700.002137162.0423450.495708(1, 237591774)
710.8084345243416.6507630.442027(6, 29944376)
720.2326685243618.6469470.603043(6, 29944151)
730.741291506315.1984730.621487(6, 32664883)
740.026316436162.3067960.784810(6, 32664926)
750.86320339531.9369020.488386(10, 4999206)
760.815908493215.2118320.928361(6, 32661393)
770.380747480191.6826920.596527(6, 32661384)
780.778990272.5810810.645061(6, 32661333)
790.00740701.3076920.481203(12, 57099758)
800.641934524353.8416030.795312(15, 90088606)
810.9939345231127.1335880.582806(16, 2106849)
820.9955225171391.3957530.989221(6, 29942795)
830.9650235102437.3996100.856497(6, 29942858)
840.0619885242200.0858780.573877(6, 29942916)
850.756602292.6145040.669605(3, 75630855)
860.224100131.7284890.588009(3, 75630794)
870.5495321037.1495100.523889(3, 49686483)
880.6836125191443.9732820.499179(6, 29943463)
890.758810353.0599610.520303(6, 29943667)
900.85811252366.9847330.899413(3, 179234284)
910.84474251388.1431300.874750(17, 7674888)
921.000000517117.5267181.000000(17, 7674256)
930.49332851282.1202290.692187(17, 7673704)
940.403970553.7862750.490953(17, 21416556)
950.666459523986.1145040.500538(8, 100709671)
960.95112500.0472440.509217(3, 183959847)
970.67140650194.8541270.794175(17, 31350209)
980.530668518380.9942750.738304(5, 68295269)
990.87078149523.5725190.462571(22, 24627926)
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100 rows × 5 columns

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auprcrnaseq_nrnaseq_rdvcfIndex
00.998211519133.822519(2, 208248388)
10.543616520122.076336(17, 7673803)
20.865149519133.375954(2, 208248389)
30.99154644838.312977(14, 32092134)
40.951786519133.375954(2, 208248389)
\n", "
" ], "text/plain": [ " auprc rnaseq_n rnaseq_rd vcfIndex\n", "0 0.998211 519 133.822519 (2, 208248388)\n", "1 0.543616 520 122.076336 (17, 7673803)\n", "2 0.865149 519 133.375954 (2, 208248389)\n", "3 0.991546 448 38.312977 (14, 32092134)\n", "4 0.951786 519 133.375954 (2, 208248389)" ] }, "execution_count": 186, "metadata": {}, "output_type": "execute_result" } ], "source": [ "praucDf.head()" ] }, { "cell_type": "code", "execution_count": 187, "metadata": {}, "outputs": [], "source": [ "import matplotlib.pyplot as plt" ] }, { "cell_type": "code", "execution_count": 188, "metadata": {}, "outputs": [ { "data": { "text/plain": [ "Text(0.5,0,'AUPRC')" ] }, "execution_count": 188, "metadata": {}, "output_type": "execute_result" }, { "data": { "image/png": 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" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "fig,ax=plt.subplots(figsize=(4,3))\n", "praucDf['auprc'].hist(ax=ax)\n", "#ax.set_yticklabels([])\n", "ax.grid(False)\n", "ax.set_yticklabels([])\n", "ax.set_ylabel('# of samples')\n", "ax.set_xlabel('AUPRC')" ] }, { "cell_type": "code", "execution_count": 189, "metadata": {}, "outputs": [ { "ename": "TypeError", "evalue": "'>' not supported between instances of 'dict' and 'float'", "output_type": "error", "traceback": [ "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", "\u001b[0;31mTypeError\u001b[0m Traceback (most recent call last)", "\u001b[0;32m\u001b[0m in \u001b[0;36m\u001b[0;34m()\u001b[0m\n\u001b[1;32m 1\u001b[0m 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y)\u001b[0m\n\u001b[1;32m 1117\u001b[0m \u001b[0mresult\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mlibops\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mvec_compare\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mx\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0my\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mop\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1118\u001b[0m \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 1119\u001b[0;31m \u001b[0mresult\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mlibops\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mscalar_compare\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mx\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0my\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mop\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 1120\u001b[0m \u001b[0;32mreturn\u001b[0m \u001b[0mresult\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1121\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n", "\u001b[0;32mpandas/_libs/ops.pyx\u001b[0m in \u001b[0;36mpandas._libs.ops.scalar_compare\u001b[0;34m()\u001b[0m\n", "\u001b[0;31mTypeError\u001b[0m: '>' not supported between instances of 'dict' and 'float'" ] } ], "source": [ "praucS=pd.Series(roc_auc_l).dropna()\n", "(praucS>0.8).mean()" ] }, { "cell_type": "code", "execution_count": 182, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/matplotlib/axes/_axes.py:6462: UserWarning: The 'normed' kwarg is deprecated, and has been replaced by the 'density' kwarg.\n", " warnings.warn(\"The 'normed' kwarg is deprecated, and has been \"\n" ] }, { "ename": "TypeError", "evalue": "'<' not supported between instances of 'dict' and 'float'", "output_type": "error", "traceback": [ "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", "\u001b[0;31mTypeError\u001b[0m Traceback (most recent call last)", 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rna-seqwxs
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" ], "text/plain": [ "Empty DataFrame\n", "Columns: [(rna-seq, ReadDepth), (rna-seq, AverageBaseQuality), (wxs, ReadDepth), (wxs, AverageBaseQuality)]\n", "Index: []" ] }, "execution_count": 99, "metadata": {}, "output_type": "execute_result" } ], "source": [ "wxsWithDataDf_base.head()" ] }, { "cell_type": "code", "execution_count": 20, "metadata": { "scrolled": true }, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:13: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", " del sys.path[0]\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:35: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:62: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n" ] } ], "source": [ "threshold=2\n", "\n", "selectedBase='T'\n", "query_chromosome, qeury_corrdinate='2',208248388\n", "m_chr=targetted_df.index.get_level_values('Chr')==query_chromosome\n", "Pos_array=targetted_df.index.get_level_values('Pos')\n", "window_size=0\n", "\n", "m_pos=(Pos_array>=(qeury_corrdinate-window_size))&(Pos_array<=(qeury_corrdinate+window_size))\n", "m_qual=targetted_df['AverageBaseQuality']>=30\n", "\n", "targetted_df_sub=targetted_df[m_pos&m_qual]\n", "\n", "index_metaDf=targetted_df_sub.index.to_frame()\n", "\n", "index_metaDf['sample_barcode']=manifest_df_w_RNA_WXS.set_index('file_id').loc[index_metaDf['Run_digits']]['sample_barcode'].values\n", "\n", "multI=index_metaDf.set_index(['sample_barcode','Run_digits','Chr','Pos','base']).index\n", "targetted_df_sub.index=multI\n", "\n", "\n", "rnaseq_uuids=manifest_df_w_RNA_WXS[manifest_df_w_RNA_WXS['experimental_strategy']=='RNA-Seq']['file_id'].unique()\n", "m_uuid=targetted_df_sub.index.get_level_values('Run_digits').isin(rnaseq_uuids)\n", "rnaseq_df=targetted_df_sub[m_uuid]\n", "\n", "groupings_L=['sample_barcode','Chr','Pos','base']\n", "\n", "rnaseq_df=rnaseq_df.groupby(groupings_L).first()\n", "\n", "wxs_uuids=manifest_df_w_RNA_WXS[manifest_df_w_RNA_WXS['experimental_strategy']=='WXS']['file_id'].unique()\n", "m_uuid=targetted_df_sub.index.get_level_values('Run_digits').isin(wxs_uuids)\n", "wxs_df=targetted_df_sub[m_uuid]\n", "\n", "wxs_df=wxs_df.groupby(groupings_L).first()\n", "\n", "mergedDf=pd.concat([ rnaseq_df,wxs_df],axis=1,keys=['rna-seq','wxs'])\n", "\n", "mergedDf['wxs']['ReadDepth']=mergedDf['wxs']['ReadDepth'].fillna(0)\n", "\n", "#mergedDf\n", "\n", "#for the whole \n", "\n", "from sklearn import metrics\n", "\n", "#### get the homozygous\n", "\n", "wxsWithDataDf=mergedDf#[mergedDf['wxs']['ReadDepth']>=threshold]\n", "\n", "sampleRdS=wxsWithDataDf['wxs'].groupby('sample_barcode')['ReadDepth'].sum()\n", "\n", "xwsSamplesWithCoverage=sampleRdS.index[sampleRdS>threshold]\n", "\n", "m_base=wxsWithDataDf.index.get_level_values('base')==selectedBase\n", "\n", "m_wxs_coverage=wxsWithDataDf.index.get_level_values('sample_barcode').isin(xwsSamplesWithCoverage)\n", "\n", "m_valid_all=mergedDf.notnull().all(axis=1)\n", "\n", "wxsWithDataDf_base=wxsWithDataDf[m_base&m_wxs_coverage]\n", "\n", "wxsWithDataDf_base['rna-seq']=wxsWithDataDf_base['rna-seq'].fillna(0)\n", "\n", "#wxsWithDataDf_base['rna-seq']['ReadDepth'].hist()\n", "\n", "#wxsWithDataDf_base['wxs']['ReadDepth'].hist()\n", "\n", "y_true=wxsWithDataDf_base['wxs']['ReadDepth']>=threshold\n", "\n", "\n", "\n", "precision,recall,_=metrics.precision_recall_curve(y_true,\n", " wxsWithDataDf_base['rna-seq']['ReadDepth'].fillna(0))\n", "auprc=metrics.auc(recall,precision)\n", "\n", "#group=wxsWithDataDf.groupby('base')\n", "\n", "#for base, df in group:\n", "# break" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "\n" ] }, { "cell_type": "code", "execution_count": 296, "metadata": { "scrolled": true }, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:3: FutureWarning: \n", "Passing list-likes to .loc or [] with any missing label will raise\n", "KeyError in the future, you can use .reindex() as an alternative.\n", "\n", "See the documentation here:\n", "https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n", " This is separate from the ipykernel package so we can avoid doing imports until\n" ] } ], "source": [ "index_metaDf=targetted_df_sub.index.to_frame()\n", "\n", "index_metaDf['sample_barcode']=manifest_df_w_RNA_WXS.set_index('file_id').loc[index_metaDf['Run_digits']]['sample_barcode'].values\n", "\n", "multI=index_metaDf.set_index(['sample_barcode','Run_digits','Chr','Pos','base']).index\n", "targetted_df_sub.index=multI\n", "\n", "wxs_df=targetted_df_sub[m_uuid]#.loc[wxs_uuid]" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [] }, { "cell_type": "code", "execution_count": 29, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "CPU times: user 72 ms, sys: 32 ms, total: 104 ms\n", "Wall time: 102 ms\n" ] } ], "source": [ "%time wxs_df=wxs_df.groupby(groupings_L).first()" ] }, { "cell_type": "code", "execution_count": 30, "metadata": {}, "outputs": [], "source": [ "rnaseq_uuids=manifest_df_w_RNA_WXS[manifest_df_w_RNA_WXS['experimental_strategy']=='RNA-Seq']['file_id'].unique()\n", "\n", "m_uuid=targetted_df_sub.index.get_level_values('Run_digits').isin(rnaseq_uuids)\n", "\n", "rnaseq_df=targetted_df_sub[m_uuid]#.loc[rnaseq_uuid]" ] }, { "cell_type": "code", "execution_count": 31, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "CPU times: user 24 ms, sys: 0 ns, total: 24 ms\n", "Wall time: 28.5 ms\n" ] } ], "source": [ "%time rnaseq_df=rnaseq_df.groupby(groupings_L).first()" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [] }, { "cell_type": "code", "execution_count": 32, "metadata": {}, "outputs": [], "source": [ "mergedDf=pd.concat([ rnaseq_df,wxs_df],axis=1,keys=['rna-seq','wxs'])" ] }, { "cell_type": "code", "execution_count": 33, "metadata": {}, "outputs": [], "source": [ "mergedDf=mergedDf[~mergedDf.isnull().all(axis=1)]" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## identify IDH1 mutations" ] }, { "cell_type": "code", "execution_count": 34, "metadata": {}, "outputs": [], "source": [ "#ref C\n", "IDH1_corrdinate=208248388\n", "mergedDf_subDf=mergedDf[mergedDf.index.get_level_values('Pos')==IDH1_corrdinate]" ] }, { "cell_type": "code", "execution_count": 35, "metadata": {}, "outputs": [], "source": [ "m_quality=(mergedDf_subDf['wxs']['AverageBaseQuality']>20)\n", "ref_alt='T'\n", "m_alt=(mergedDf_subDf.index.get_level_values('base'))==ref_alt\n", "\n", "qualFilteredDf=mergedDf_subDf[m_quality]" ] }, { "cell_type": "code", "execution_count": 36, "metadata": {}, "outputs": [], "source": [ "unstackDf=qualFilteredDf.unstack()" ] }, { "cell_type": "code", "execution_count": 37, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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baseACGTACGTACGTACGT
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" ], "text/plain": [ " rna-seq \\\n", "features ReadDepth AverageBaseQuality \n", "base A C G T A \n", "sample_barcode Chr Pos \n", "TCGA-CS-4938-01B 2 208248388 NaN 68.0 NaN 24.0 NaN \n", "TCGA-CS-4941-01A 2 208248388 NaN 235.0 NaN NaN NaN \n", "TCGA-CS-4942-01A 2 208248388 NaN 140.0 NaN 19.0 NaN \n", "TCGA-CS-4944-01A 2 208248388 NaN 43.0 NaN 17.0 NaN \n", "TCGA-CS-5390-01A 2 208248388 NaN 95.0 NaN 32.0 NaN \n", "\n", " wxs \\\n", "features ReadDepth \n", "base C G T A C G T \n", "sample_barcode Chr Pos \n", "TCGA-CS-4938-01B 2 208248388 37.0 NaN 38.0 NaN 87.0 NaN 29.0 \n", "TCGA-CS-4941-01A 2 208248388 37.0 NaN NaN NaN 182.0 NaN NaN \n", "TCGA-CS-4942-01A 2 208248388 38.0 NaN 38.0 NaN 192.0 NaN 46.0 \n", "TCGA-CS-4944-01A 2 208248388 37.0 NaN 37.0 NaN 149.0 NaN 43.0 \n", "TCGA-CS-5390-01A 2 208248388 37.0 NaN 38.0 NaN 141.0 NaN 51.0 \n", "\n", " \n", "features AverageBaseQuality \n", "base A C G T \n", "sample_barcode Chr Pos \n", "TCGA-CS-4938-01B 2 208248388 NaN 29.0 NaN 29.0 \n", "TCGA-CS-4941-01A 2 208248388 NaN 27.0 NaN NaN \n", "TCGA-CS-4942-01A 2 208248388 NaN 25.0 NaN 28.0 \n", "TCGA-CS-4944-01A 2 208248388 NaN 27.0 NaN 28.0 \n", "TCGA-CS-5390-01A 2 208248388 NaN 26.0 NaN 27.0 " ] }, "execution_count": 37, "metadata": {}, "output_type": "execute_result" } ], "source": [ "unstackDf.head()" ] }, { "cell_type": "code", "execution_count": 38, "metadata": {}, "outputs": [], "source": [ "from sklearn import metrics" ] }, { "cell_type": "code", "execution_count": 39, "metadata": {}, "outputs": [], "source": [ "import matplotlib.pyplot as plt" ] }, { "cell_type": "code", "execution_count": 45, "metadata": {}, "outputs": [ { "data": { "image/png": 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\n", 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" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "\n", "fig,ax=plt.subplots(figsize=(5,3))\n", "\n", "unstackDf[('wxs','ReadDepth','T')].fillna(0).hist(bins=30,label='Minor alle',ax=ax)\n", "unstackDf[('wxs','ReadDepth','C')].fillna(0).hist(bins=30,ax=ax,\n", " label='Reference allele')\n", "ax.axvline(x=10,c='red')\n", "ax.set_ylabel('# of tumor samples')\n", "ax.legend()\n", "ax.set_xlabel('Allelic read counts')\n", "ax.grid(False)\n" ] }, { "cell_type": "code", "execution_count": 48, "metadata": {}, "outputs": [ { "data": { "text/plain": [ "351" ] }, "execution_count": 48, "metadata": {}, "output_type": "execute_result" } ], "source": [ "(unstackDf[('wxs','ReadDepth','T')]>0).sum()" ] }, { "cell_type": "code", "execution_count": 41, "metadata": {}, "outputs": [ { "ename": "NameError", "evalue": "name 'asdasdas' is not defined", "output_type": "error", "traceback": [ "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", "\u001b[0;31mNameError\u001b[0m Traceback (most recent call last)", "\u001b[0;32m\u001b[0m in \u001b[0;36m\u001b[0;34m()\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0masdasdas\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m", "\u001b[0;31mNameError\u001b[0m: name 'asdasdas' is not defined" ] } ], "source": [ "asdasdas" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "y_true=(>10)" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "y_true.value_counts()" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "print ('ROC AUC',metrics.roc_auc_score(y_true,\n", " unstackDf[('rna-seq','ReadDepth','T')].fillna(0)))\n", "precision, recall, thresholds=metrics.precision_recall_curve(y_true,\n", " unstackDf[('rna-seq','ReadDepth','T')].fillna(0))\n", "ax=pd.DataFrame({'precision':precision,'recall':recall}).plot(x='recall',y='precision')\n", "ax.set_ylabel('Precision')\n", "ax.set_xlabel('Recall')\n", "metrics.auc(recall,precision)\n", "ax.set_title('IDH1 C>T mutation using RNAseq')" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "import seaborn as sns" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "qualFilteredDf[('wxs','ReadDepth')].index.get_level_values('base').value_counts()" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "qualFilteredDf[('rna-seq','ReadDepth')].index.get_level_values('base').value_counts()" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "qualFilteredDf[('rna-seq','ReadDepth')].index.get_level_values('base').value_counts()" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "mergedDf_subDf" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "\n", "qualFilteredDf['ReadDepth'],qualFilteredDf['wxs']>3" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "##c \n" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "#qualFilteredDf[]" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "unstackDf=qualFilteredDf['wxs'].unstack()['ReadDepth']" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "#qualFilteredDf['wxs'].unstack()['ReadDepth']" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "sns.jointplot(data=qualFilteredDf[qualFilteredDf.index.get_level_values('base')=='T'],x=('rna-seq','ReadDepth'),y=('wxs','ReadDepth'))\n" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "#categorical_crossentropy" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "### generate the correlation between the data " ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [] } ], "metadata": { "kernelspec": { "display_name": "Python 3", "language": "python", "name": "python3" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.6.5" } }, "nbformat": 4, "nbformat_minor": 2 }