{ "metadata": { "name": "", "signature": "sha256:36b66e8a7a4081028507217b6e2b49b63f9448d00531828ed6a511592ea2815a" }, "nbformat": 3, "nbformat_minor": 0, "worksheets": [ { "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "#DNA methylation of Oyster Sperm based on Genomic Features" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "_methratio_ file in SQLShare\n", "" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### BiGO methratio GFF\n", "\n", "```\n", "SELECT \n", "chr as seqname, \n", "'methratio' as source, \n", "'CpG' as feature, \n", "pos as start,\n", "pos + 1 as [end],\n", "ratio as score, \n", "strand, \n", "'.' as frame, \n", "'.' as attribute \n", "FROM [sr320@washington.edu].[clean_BiGo_methratio_v1]\n", "where \n", "context like '__CG_' \n", "and\n", "CT_Count >= 5\n", "```\n", "\n", "" ] }, { "cell_type": "code", "collapsed": false, "input": [ "# ie python fetchdata.py -d \"[sr320@washington.edu].[BiGO_Methylation_oysterv9_GFF]\u200b\" -f tsv -o /Volumes/web/cnidarian/BiGO_Methylation10x_oysterv9.gff\n", "\n", "# running on commandline because cannot get to work in IPython" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 13 }, { "cell_type": "raw", "metadata": {}, "source": [ "python fetchdata.py -d \"[sr320@washington.edu].[BiGo_methratio_GFF_boop]\u200b\" -f tsv -o /Volumes/web/cnidarian/BiGo_methratio_boop.gff" ] }, { "cell_type": "code", "collapsed": false, "input": [ "#fetchdata failed" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 15 }, { "cell_type": "code", "collapsed": false, "input": [ "#Dowloaded csv\n", "# should be same as \n", "!head /Volumes/web/cnidarian/BiGO_Methylation5x_oysterv9.gff" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "seqname\tsource\tfeature\tstart\tend\tscore\tstrand\tframe\tattribute\r", "\r\n", "C10005\tmethratio\tCpG\t57\t58\t0.000\t+\t.\t.\r", "\r\n", "C10009\tmethratio\tCpG\t70\t71\t0.000\t+\t.\t.\r", "\r\n", "C10009\tmethratio\tCpG\t124\t125\t0.000\t+\t.\t.\r", "\r\n", "C10009\tmethratio\tCpG\t128\t129\t0.000\t+\t.\t.\r", "\r\n", "C10009\tmethratio\tCpG\t136\t137\t0.000\t+\t.\t.\r", "\r\n", "C10011\tmethratio\tCpG\t51\t52\t0.000\t+\t.\t.\r", "\r\n", "C10011\tmethratio\tCpG\t62\t63\t0.000\t+\t.\t.\r", "\r\n", "C10011\tmethratio\tCpG\t101\t102\t0.000\t+\t.\t.\r", "\r\n", "C10011\tmethratio\tCpG\t108\t109\t0.000\t+\t.\t.\r", "\r\n" ] } ], "prompt_number": 16 }, { "cell_type": "code", "collapsed": false, "input": [ "!wc /Volumes/web/cnidarian/BiGO_Methylation5x_oysterv9.gff" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ " 7648305 68834745 402812022 /Volumes/web/cnidarian/BiGO_Methylation5x_oysterv9.gff\r\n" ] } ], "prompt_number": 17 }, { "cell_type": "code", "collapsed": false, "input": [ "!head /Volumes/web/cnidarian/BiGo_methratio_boop.gff" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "seqname\tsource\tfeature\tstart\tend\tscore\tstrand\tframe\tattribute\r", "\r\n", "C10005\tmethratio\tCpG\t57\t58\t0\t+\t.\t.\r", "\r\n", "C10009\tmethratio\tCpG\t70\t71\t0\t+\t.\t.\r", "\r\n", "C10009\tmethratio\tCpG\t124\t125\t0\t+\t.\t.\r", "\r\n", "C10009\tmethratio\tCpG\t128\t129\t0\t+\t.\t.\r", "\r\n", "C10009\tmethratio\tCpG\t136\t137\t0\t+\t.\t.\r", "\r\n", "C10011\tmethratio\tCpG\t51\t52\t0\t+\t.\t.\r", "\r\n", "C10011\tmethratio\tCpG\t62\t63\t0\t+\t.\t.\r", "\r\n", "C10011\tmethratio\tCpG\t101\t102\t0\t+\t.\t.\r", "\r\n", "C10011\tmethratio\tCpG\t108\t109\t0\t+\t.\t.\r", "\r\n" ] } ], "prompt_number": 1 }, { "cell_type": "code", "collapsed": false, "input": [ "!wc /Volumes/web/cnidarian/BiGo_methratio_boop.gff" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ " 7642817 68785353 378876013 /Volumes/web/cnidarian/BiGo_methratio_boop.gff\r\n" ] } ], "prompt_number": 21 }, { "cell_type": "code", "collapsed": false, "input": [ "from pandas import *\n", "\n", "# read data from data file into a pandas DataFrame \n", "BiGOboop = read_csv(\"http://eagle.fish.washington.edu/cnidarian/BiGo_methratio_GFF_boop.csv\", # name of the data file\n", " sep=\",\", # what character separates each column?\n", " na_values=[\"\", \" \"]) # what values should be considered \"blank\" values?" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 125 }, { "cell_type": "code", "collapsed": false, "input": [ "BiGOboop['score'].hist(bins=50);\n", "#Axis limits are changed using the axis([xmin, xmax, ymin, ymax]) function.\n", "plt.axis([0, 1, 0, 400000])\n" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "pyout", "prompt_number": 126, "text": [ "[0, 1, 0, 400000]" ] }, { "output_type": "display_data", "png": 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pHDhwICQvNpo99dRT4R5CxFAWNmVhUxYhYqbQ3NxsPvnkE5ORkWG1bd++3fz0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\nNBUNEREJ2v8HpU2xb+zUnHoAAAAASUVORK5CYII=\n" } ], "prompt_number": 126 }, { "cell_type": "markdown", "metadata": {}, "source": [ "---\n", "### CG motif " ] }, { "cell_type": "code", "collapsed": false, "input": [ "!head /Volumes/web/cnidarian/TJGR_oyster_v9_CGmotif.gff" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "##gff-version 2.0\r\n", "##date 2013-04-23\r\n", "##Type DNA scaffold360\r\n", "scaffold360\tfuzznuc\tmisc_feature\t60\t61\t2.000\t+\t.\tSequence \"scaffold360.1\" ; note \"*pat pattern1\"\r\n", "scaffold360\tfuzznuc\tmisc_feature\t96\t97\t2.000\t+\t.\tSequence \"scaffold360.2\" ; note \"*pat pattern1\"\r\n", "scaffold360\tfuzznuc\tmisc_feature\t120\t121\t2.000\t+\t.\tSequence \"scaffold360.3\" ; note \"*pat pattern1\"\r\n", "scaffold360\tfuzznuc\tmisc_feature\t187\t188\t2.000\t+\t.\tSequence \"scaffold360.4\" ; note \"*pat pattern1\"\r\n", "##gff-version 2.0\r\n", "##date 2013-04-23\r\n", "##Type DNA scaffold18356\r\n" ] } ], "prompt_number": 29 }, { "cell_type": "code", "collapsed": false, "input": [ "!fgrep -c \"fuzznuc\" /Volumes/web/cnidarian/TJGR_oyster_v9_CGmotif.gff" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "5625744\r\n" ] } ], "prompt_number": 30 }, { "cell_type": "code", "collapsed": false, "input": [ "!head /Volumes/web/cnidarian/TJGR_oyster_v9_CG.gff\n" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "##gff-version 3\r\n", "##sequence-region scaffold360 1 280\r\n", "#!Date 2013-04-23\r\n", "#!Type DNA\r\n", "#!Source-version EMBOSS 6.5.7.0\r\n", "scaffold360\tfuzznuc\tnucleotide_motif\t60\t61\t2\t+\t.\tID=scaffold360.1;note=*pat pattern:CG\r\n", "scaffold360\tfuzznuc\tnucleotide_motif\t96\t97\t2\t+\t.\tID=scaffold360.2;note=*pat pattern:CG\r\n", "scaffold360\tfuzznuc\tnucleotide_motif\t120\t121\t2\t+\t.\tID=scaffold360.3;note=*pat pattern:CG\r\n", "scaffold360\tfuzznuc\tnucleotide_motif\t187\t188\t2\t+\t.\tID=scaffold360.4;note=*pat pattern:CG\r\n", "##gff-version 3\r\n" ] } ], "prompt_number": 31 }, { "cell_type": "code", "collapsed": false, "input": [ "!fgrep -c \"fuzznuc\" /Volumes/web/cnidarian/TJGR_oyster_v9_CG.gff" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "9978551\r\n" ] } ], "prompt_number": 32 }, { "cell_type": "markdown", "metadata": {}, "source": [ "---\n", "###Confirming CG\n" ] }, { "cell_type": "code", "collapsed": false, "input": [ "#ran before\n", "!head /Volumes/web/cnidarian/oyster_v9_CG_fuzznuc.output" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "########################################\r\n", "# Program: fuzznuc\r\n", "# Rundate: Fri 19 Apr 2013 14:58:14\r\n", "# Commandline: fuzznuc\r\n", "# -sequence oyster.v9.fa\r\n", "# -pattern CG\r\n", "# -outfile fuzznuc.output\r\n", "# Report_format: seqtable\r\n", "# Report_file: fuzznuc.output\r\n", "########################################\r\n" ] } ], "prompt_number": 7 }, { "cell_type": "code", "collapsed": false, "input": [ "!fgrep -c \"+ pattern: \" /Volumes/web/cnidarian/oyster_v9_CG_fuzznuc.output" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "9978551\r\n" ] } ], "prompt_number": 9 }, { "cell_type": "code", "collapsed": false, "input": [ "!fgrep -c \"nucleotide_motif\" /Volumes/web/bivalvia/wholegenomefiles_MBDbsSeq_gill/gffs/TJGR_oyster_v9_CG.gff" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "9978551\r\n" ] } ], "prompt_number": 10 }, { "cell_type": "markdown", "metadata": {}, "source": [ "---\n", "###CG Content in all Features" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "---" ] }, { "cell_type": "code", "collapsed": false, "input": [ "!intersectbed -a /Volumes/web/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_exon.gff -b /Volumes/web/cnidarian/TJGR_oyster_v9_CG.gff -c > /Volumes/web/cnidarian/TGR_intersectbed_CDS_v9_CGmotif.txt " ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 78 }, { "cell_type": "code", "collapsed": false, "input": [ "!intersectbed -b /Volumes/web/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_exon.gff -a /Volumes/web/cnidarian/TJGR_oyster_v9_CG.gff > /Volumes/web/cnidarian/TGR_CGmotif_intersect_exon.txt " ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 80 }, { "cell_type": "code", "collapsed": false, "input": [ "!head /Volumes/web/cnidarian/TGR_intersectbed_CDS_v9_CGmotif.txt" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "C16582\tGLEAN\tCDS\t35\t385\t.\t-\t0\tParent=CGI_10000001;\t14\r\n", "C17212\tGLEAN\tCDS\t31\t363\t.\t+\t0\tParent=CGI_10000002;\t6\r\n", "C17316\tGLEAN\tCDS\t30\t257\t.\t+\t0\tParent=CGI_10000003;\t10\r\n", "C17476\tGLEAN\tCDS\t104\t257\t.\t-\t0\tParent=CGI_10000004;\t5\r\n", "C17476\tGLEAN\tCDS\t34\t74\t.\t-\t2\tParent=CGI_10000004;\t2\r\n", "C17998\tGLEAN\tCDS\t196\t387\t.\t-\t0\tParent=CGI_10000005;\t11\r\n", "C18346\tGLEAN\tCDS\t174\t551\t.\t+\t0\tParent=CGI_10000009;\t29\r\n", "C18428\tGLEAN\tCDS\t286\t546\t.\t-\t0\tParent=CGI_10000010;\t24\r\n", "C18964\tGLEAN\tCDS\t203\t658\t.\t-\t0\tParent=CGI_10000011;\t9\r\n", "C18980\tGLEAN\tCDS\t30\t674\t.\t+\t0\tParent=CGI_10000012;\t56\r\n" ] } ], "prompt_number": 37 }, { "cell_type": "code", "collapsed": false, "input": [ "!wc /Volumes/web/cnidarian/TGR_intersectbed_CDS_v9_CGmotif.txt" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ " 196691 1966910 12782384 /Volumes/web/cnidarian/TGR_intersectbed_CDS_v9_CGmotif.txt\r\n" ] } ], "prompt_number": 76 }, { "cell_type": "code", "collapsed": false, "input": [ "cat /Volumes/web/cnidarian/TGR_intersectbed_CDS_v9_CGmotif.txt | awk -F\"\\t\" '{ sum+=$10} END {print sum}'" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "1134622\r\n" ] } ], "prompt_number": 43 }, { "cell_type": "code", "collapsed": false, "input": [ "!head /Volumes/web/cnidarian/TGR_CGmotif_intersect_exon.txt" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "scaffold350\tfuzznuc\tnucleotide_motif\t1161\t1162\t2\t+\t.\tID=scaffold350.25;note=*pat pattern:CG\r\n", "scaffold350\tfuzznuc\tnucleotide_motif\t1183\t1184\t2\t+\t.\tID=scaffold350.26;note=*pat pattern:CG\r\n", "scaffold350\tfuzznuc\tnucleotide_motif\t1200\t1201\t2\t+\t.\tID=scaffold350.27;note=*pat pattern:CG\r\n", "scaffold350\tfuzznuc\tnucleotide_motif\t1252\t1253\t2\t+\t.\tID=scaffold350.28;note=*pat pattern:CG\r\n", "scaffold350\tfuzznuc\tnucleotide_motif\t1267\t1268\t2\t+\t.\tID=scaffold350.29;note=*pat pattern:CG\r\n", "scaffold350\tfuzznuc\tnucleotide_motif\t1287\t1288\t2\t+\t.\tID=scaffold350.30;note=*pat pattern:CG\r\n", "scaffold350\tfuzznuc\tnucleotide_motif\t1331\t1332\t2\t+\t.\tID=scaffold350.31;note=*pat pattern:CG\r\n", "scaffold350\tfuzznuc\tnucleotide_motif\t1416\t1417\t2\t+\t.\tID=scaffold350.32;note=*pat pattern:CG\r\n", "scaffold350\tfuzznuc\tnucleotide_motif\t1439\t1440\t2\t+\t.\tID=scaffold350.33;note=*pat pattern:CG\r\n", "scaffold350\tfuzznuc\tnucleotide_motif\t1480\t1481\t2\t+\t.\tID=scaffold350.34;note=*pat pattern:CG\r\n" ] } ], "prompt_number": 81 }, { "cell_type": "code", "collapsed": false, "input": [ "!wc /Volumes/web/cnidarian/TGR_CGmotif_intersect_exon.txt" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ " 1134622 11346220 111446503 /Volumes/web/cnidarian/TGR_CGmotif_intersect_exon.txt\r\n" ] } ], "prompt_number": 82 }, { "cell_type": "code", "collapsed": false, "input": [ "## CG intersect intron\n", "!intersectbed -a /Volumes/web/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_CG.gff -b /Volumes/web/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_intron.gff > /Volumes/web/cnidarian/TGR_intersectbed_intron_v9_CG.gff" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 86 }, { "cell_type": "code", "collapsed": false, "input": [ "!wc /Volumes/web/cnidarian/TGR_intersectbed_intron_v9_CG.gff" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ " 2886432 28864320 283836671 /Volumes/web/cnidarian/TGR_intersectbed_intron_v9_CG.gff\r\n" ] } ], "prompt_number": 87 }, { "cell_type": "code", "collapsed": false, "input": [ "## CG intersect TE\n", "!intersectbed -a /Volumes/web/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_CG.gff -b /Volumes/web/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_TE.gff > /Volumes/web/cnidarian/TGR_intersectbed_CG_TE.gff" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 88 }, { "cell_type": "code", "collapsed": false, "input": [ "!wc /Volumes/web/cnidarian/TGR_intersectbed_CG_TE.gff" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ " 832569 8325690 81351343 /Volumes/web/cnidarian/TGR_intersectbed_CG_TE.gff\r\n" ] } ], "prompt_number": 89 }, { "cell_type": "code", "collapsed": false, "input": [ "## CG intersect Promoter\n", "!intersectbed -a /Volumes/web/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_CG.gff -b /Volumes/web/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_1k5p_gene_promoter.gff > /Volumes/web/cnidarian/TGR_intersectbed_CG_prom.gff" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 90 }, { "cell_type": "code", "collapsed": false, "input": [ "!wc /Volumes/web/cnidarian/TGR_intersectbed_CG_prom.gff" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ " 616223 6162230 60375672 /Volumes/web/cnidarian/TGR_intersectbed_CG_prom.gff\r\n" ] } ], "prompt_number": 91 }, { "cell_type": "code", "collapsed": false, "input": [ "!head /Volumes/web/cnidarian/TGR_intersectbed_CG_prom.gff" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "scaffold350\tfuzznuc\tnucleotide_motif\t3250\t3251\t2\t+\t.\tID=scaffold350.82;note=*pat pattern:CG\r\n", "scaffold350\tfuzznuc\tnucleotide_motif\t3266\t3267\t2\t+\t.\tID=scaffold350.83;note=*pat pattern:CG\r\n", "scaffold350\tfuzznuc\tnucleotide_motif\t3299\t3300\t2\t+\t.\tID=scaffold350.84;note=*pat pattern:CG\r\n", "scaffold350\tfuzznuc\tnucleotide_motif\t3316\t3317\t2\t+\t.\tID=scaffold350.85;note=*pat pattern:CG\r\n", "scaffold350\tfuzznuc\tnucleotide_motif\t3384\t3385\t2\t+\t.\tID=scaffold350.86;note=*pat pattern:CG\r\n", "scaffold350\tfuzznuc\tnucleotide_motif\t3474\t3475\t2\t+\t.\tID=scaffold350.87;note=*pat pattern:CG\r\n", "scaffold350\tfuzznuc\tnucleotide_motif\t3497\t3498\t2\t+\t.\tID=scaffold350.88;note=*pat pattern:CG\r\n", "scaffold350\tfuzznuc\tnucleotide_motif\t3505\t3506\t2\t+\t.\tID=scaffold350.89;note=*pat pattern:CG\r\n", "scaffold350\tfuzznuc\tnucleotide_motif\t3608\t3609\t2\t+\t.\tID=scaffold350.90;note=*pat pattern:CG\r\n", "scaffold350\tfuzznuc\tnucleotide_motif\t3622\t3623\t2\t+\t.\tID=scaffold350.91;note=*pat pattern:CG\r\n" ] } ], "prompt_number": 1 }, { "cell_type": "code", "collapsed": false, "input": [ "## CG intersect Promoter\n", "!intersectbed -a /Volumes/web/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_CG.gff -b /Volumes/web/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_COMP_gene_prom_TE.bed > /Volumes/web/cnidarian/TGR_intersectbed_CG_other.gff" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 92 }, { "cell_type": "code", "collapsed": false, "input": [ "!wc /Volumes/web/cnidarian/TGR_intersectbed_CG_other.gff" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ " 5121236 51212360 499097421 /Volumes/web/cnidarian/TGR_intersectbed_CG_other.gff\r\n" ] } ], "prompt_number": 93 }, { "cell_type": "markdown", "metadata": {}, "source": [ "--- \n", "##mCG per feature\n", "\n", "\n", " SELECT \n", " chr as seqname, \n", " 'methratio' as source, \n", " 'CpG' as feature, \n", " pos as start,\n", " pos + 1 as [end],\n", " ratio as score, \n", " strand, \n", " '.' as frame, \n", " '.' as attribute \n", " FROM [sr320@washington.edu].[clean_BiGo_methratio_v1]\u200b\n", " where \n", " context like '__CG_' \n", " and\n", " CT_Count >= 5\n", " and\n", " ratio >= 0.5\n", "\n" ] }, { "cell_type": "code", "collapsed": false, "input": [ "!head /Volumes/web/cnidarian/BiGo_methratio_mCG.csv" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "seqname,source,feature,start,end,score,strand,frame,attribute\r", "\r\n", "C10093,methratio,CpG,107,108,1,+,.,.\r", "\r\n", "C10137,methratio,CpG,18,19,0.733,+,.,.\r", "\r\n", "C10137,methratio,CpG,30,31,0.778,+,.,.\r", "\r\n", "C10137,methratio,CpG,39,40,0.783,+,.,.\r", "\r\n", "C10137,methratio,CpG,72,73,0.524,+,.,.\r", "\r\n", "C10137,methratio,CpG,81,82,0.692,+,.,.\r", "\r\n", "C10137,methratio,CpG,97,98,0.556,+,.,.\r", "\r\n", "C10311,methratio,CpG,56,57,1,+,.,.\r", "\r\n", "C10671,methratio,CpG,22,23,0.5,+,.,.\r", "\r\n" ] } ], "prompt_number": 103 }, { "cell_type": "code", "collapsed": false, "input": [ "!wc /Volumes/web/cnidarian/BiGo_methratio_mCG.csv" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ " 1159721 1159721 59922755 /Volumes/web/cnidarian/BiGo_methratio_mCG.csv\r\n" ] } ], "prompt_number": 104 }, { "cell_type": "code", "collapsed": false, "input": [ "!tr ',' \"\\t\" /Volumes/web/cnidarian/BiGo_methratio_mCG.gff" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 105 }, { "cell_type": "code", "collapsed": false, "input": [ "!head /Volumes/web/cnidarian/BiGo_methratio_mCG.gff" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "seqname\tsource\tfeature\tstart\tend\tscore\tstrand\tframe\tattribute\r", "\r\n", "C10093\tmethratio\tCpG\t107\t108\t1\t+\t.\t.\r", "\r\n", "C10137\tmethratio\tCpG\t18\t19\t0.733\t+\t.\t.\r", "\r\n", "C10137\tmethratio\tCpG\t30\t31\t0.778\t+\t.\t.\r", "\r\n", "C10137\tmethratio\tCpG\t39\t40\t0.783\t+\t.\t.\r", "\r\n", "C10137\tmethratio\tCpG\t72\t73\t0.524\t+\t.\t.\r", "\r\n", "C10137\tmethratio\tCpG\t81\t82\t0.692\t+\t.\t.\r", "\r\n", "C10137\tmethratio\tCpG\t97\t98\t0.556\t+\t.\t.\r", "\r\n", "C10311\tmethratio\tCpG\t56\t57\t1\t+\t.\t.\r", "\r\n", "C10671\tmethratio\tCpG\t22\t23\t0.5\t+\t.\t.\r", "\r\n" ] } ], "prompt_number": 106 }, { "cell_type": "code", "collapsed": false, "input": [ "!tail -n +2 /Volumes/web/cnidarian/BiGo_methratio_mCG.gff > /Volumes/web/cnidarian/BiGo_methratio_mCG_tail.gff" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 107 }, { "cell_type": "code", "collapsed": false, "input": [ "!head /Volumes/web/cnidarian/BiGo_methratio_mCG_tail.gff" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "C10093\tmethratio\tCpG\t107\t108\t1\t+\t.\t.\r", "\r\n", "C10137\tmethratio\tCpG\t18\t19\t0.733\t+\t.\t.\r", "\r\n", "C10137\tmethratio\tCpG\t30\t31\t0.778\t+\t.\t.\r", "\r\n", "C10137\tmethratio\tCpG\t39\t40\t0.783\t+\t.\t.\r", "\r\n", "C10137\tmethratio\tCpG\t72\t73\t0.524\t+\t.\t.\r", "\r\n", "C10137\tmethratio\tCpG\t81\t82\t0.692\t+\t.\t.\r", "\r\n", "C10137\tmethratio\tCpG\t97\t98\t0.556\t+\t.\t.\r", "\r\n", "C10311\tmethratio\tCpG\t56\t57\t1\t+\t.\t.\r", "\r\n", "C10671\tmethratio\tCpG\t22\t23\t0.5\t+\t.\t.\r", "\r\n", "C10671\tmethratio\tCpG\t152\t153\t0.5\t+\t.\t.\r", "\r\n" ] } ], "prompt_number": 109 }, { "cell_type": "code", "collapsed": false, "input": [ "###mCG intersects with genome features" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 110 }, { "cell_type": "code", "collapsed": false, "input": [ "!intersectbed -a /Volumes/web/cnidarian/BiGo_methratio_mCG_tail.gff -b /Volumes/web/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_exon.gff > /Volumes/web/cnidarian/TGR_mCG_intersect_exon.gff" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 111 }, { "cell_type": "code", "collapsed": false, "input": [ "!wc /Volumes/web/cnidarian/TGR_mCG_intersect_exon.gff" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ " 343032 3087288 17692941 /Volumes/web/cnidarian/TGR_mCG_intersect_exon.gff\r\n" ] } ], "prompt_number": 121 }, { "cell_type": "code", "collapsed": false, "input": [ "!intersectbed -a /Volumes/web/cnidarian/BiGo_methratio_mCG_tail.gff -b /Volumes/web/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_intron.gff > /Volumes/web/cnidarian/TGR_mCG_intersect_intron.gff" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 113 }, { "cell_type": "code", "collapsed": false, "input": [ "!wc /Volumes/web/cnidarian/TGR_mCG_intersect_intron.gff" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ " 518734 4668606 26896216 /Volumes/web/cnidarian/TGR_mCG_intersect_intron.gff\r\n" ] } ], "prompt_number": 114 }, { "cell_type": "code", "collapsed": false, "input": [ "!intersectbed -a /Volumes/web/cnidarian/BiGo_methratio_mCG_tail.gff -b /Volumes/web/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_TE.gff > /Volumes/web/cnidarian/TGR_mCG_intersect_TE.gff" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 115 }, { "cell_type": "code", "collapsed": false, "input": [ "!wc /Volumes/web/cnidarian/TGR_mCG_intersect_TE.gff" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ " 38532 346788 1994156 /Volumes/web/cnidarian/TGR_mCG_intersect_TE.gff\r\n" ] } ], "prompt_number": 116 }, { "cell_type": "code", "collapsed": false, "input": [ "!intersectbed -a /Volumes/web/cnidarian/BiGo_methratio_mCG_tail.gff -b /Volumes/web/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_1k5p_gene_promoter.gff > /Volumes/web/cnidarian/TGR_mCG_intersect_prom.gff" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 117 }, { "cell_type": "code", "collapsed": false, "input": [ "!wc /Volumes/web/cnidarian/TGR_mCG_intersect_prom.gff" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ " 45241 407169 2336384 /Volumes/web/cnidarian/TGR_mCG_intersect_prom.gff\r\n" ] } ], "prompt_number": 118 }, { "cell_type": "code", "collapsed": false, "input": [ "!intersectbed -a /Volumes/web/cnidarian/BiGo_methratio_mCG_tail.gff -b /Volumes/web/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_COMP_gene_prom_TE.bed > /Volumes/web/cnidarian/TGR_mCG_intersect_other.gff" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 119 }, { "cell_type": "code", "collapsed": false, "input": [ "!wc /Volumes/web/cnidarian/TGR_mCG_intersect_other.gff" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ " 277587 2498283 14287492 /Volumes/web/cnidarian/TGR_mCG_intersect_other.gff\r\n" ] } ], "prompt_number": 120 }, { "cell_type": "markdown", "metadata": {}, "source": [ "--- \n", "\n", "\n", "\n", "\n", " \n", "\n", " \n", "\n", "\n", "\n", "\n", "\n", "\n", " \n", "\n", "\n", "\n", "\n", " \n", "\n", " \n", "\n", "\n", "\n", "\n", " \n", "\n", " \n", "\n", "\n", "\n", "\n", " \n", "\n", " \n", "\n", "\n", "\n", "\n", " \n", "\n", " \n", " \n", "
FeatureNo. FeaturesCGmCGNmCG
Exons1966911134622343032NmCG
Intron1760492886432518734NmCG
TE11978683256938532NmCG
Promoter2802361622345241NmCG
Other817365121236277587NmCG
" ] }, { "cell_type": "code", "collapsed": false, "input": [ "sum(1134622+2886432+616223+5121236)" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "pyout", "prompt_number": 99, "text": [ "9758513" ] } ], "prompt_number": 99 }, { "cell_type": "markdown", "metadata": {}, "source": [ "---\n", "\n", "##Histogram for all features" ] }, { "cell_type": "code", "collapsed": false, "input": [ "!tail -n +2 /Volumes/web/cnidarian/BiGo_methratio_boop.gff > /Volumes/web/cnidarian/BiGo_methratio_boop_c.gff" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 5 }, { "cell_type": "code", "collapsed": false, "input": [ "!head /Volumes/web/cnidarian/BiGo_methratio_boop_c.gff" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "C10005\tmethratio\tCpG\t57\t58\t0\t+\t.\t.\r", "\r\n", "C10009\tmethratio\tCpG\t70\t71\t0\t+\t.\t.\r", "\r\n", "C10009\tmethratio\tCpG\t124\t125\t0\t+\t.\t.\r", "\r\n", "C10009\tmethratio\tCpG\t128\t129\t0\t+\t.\t.\r", "\r\n", "C10009\tmethratio\tCpG\t136\t137\t0\t+\t.\t.\r", "\r\n", "C10011\tmethratio\tCpG\t51\t52\t0\t+\t.\t.\r", "\r\n", "C10011\tmethratio\tCpG\t62\t63\t0\t+\t.\t.\r", "\r\n", "C10011\tmethratio\tCpG\t101\t102\t0\t+\t.\t.\r", "\r\n", "C10011\tmethratio\tCpG\t108\t109\t0\t+\t.\t.\r", "\r\n", "C10011\tmethratio\tCpG\t115\t116\t0\t+\t.\t.\r", "\r\n" ] } ], "prompt_number": 6 }, { "cell_type": "code", "collapsed": false, "input": [ "!wc /Volumes/web/cnidarian/BiGo_methratio_boop_c.gff" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ " 7642816 68785344 378875950 /Volumes/web/cnidarian/BiGo_methratio_boop_c.gff\r\n" ] } ], "prompt_number": 7 }, { "cell_type": "code", "collapsed": false, "input": [ "!wc /Volumes/web/cnidarian/BiGo_methratio_boop.gff" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ " 7642817 68785353 378876013 /Volumes/web/cnidarian/BiGo_methratio_boop.gff\r\n" ] } ], "prompt_number": 8 }, { "cell_type": "code", "collapsed": false, "input": [ "!intersectbed -a /Volumes/web/cnidarian/oyster.v9.glean.final.rename.CDS.gff -b /Volumes/web/cnidarian/BiGo_methratio_boop_c.gff -c > /Volumes/web/cnidarian/BiGo_CDS_v9_intersect_methratio_boop.txt " ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 11 }, { "cell_type": "code", "collapsed": false, "input": [ "!head /Volumes/web/cnidarian/BiGo_CDS_v9_intersect_methratio_boop.txt " ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "C16582\tGLEAN\tCDS\t35\t385\t.\t-\t0\tParent=CGI_10000001;\t0\r\n", "C17212\tGLEAN\tCDS\t31\t363\t.\t+\t0\tParent=CGI_10000002;\t4\r\n", "C17316\tGLEAN\tCDS\t30\t257\t.\t+\t0\tParent=CGI_10000003;\t9\r\n", "C17476\tGLEAN\tCDS\t104\t257\t.\t-\t0\tParent=CGI_10000004;\t5\r\n", "C17476\tGLEAN\tCDS\t34\t74\t.\t-\t2\tParent=CGI_10000004;\t1\r\n", "C17998\tGLEAN\tCDS\t196\t387\t.\t-\t0\tParent=CGI_10000005;\t11\r\n", "C18346\tGLEAN\tCDS\t174\t551\t.\t+\t0\tParent=CGI_10000009;\t0\r\n", "C18428\tGLEAN\tCDS\t286\t546\t.\t-\t0\tParent=CGI_10000010;\t0\r\n", "C18964\tGLEAN\tCDS\t203\t658\t.\t-\t0\tParent=CGI_10000011;\t9\r\n", "C18980\tGLEAN\tCDS\t30\t674\t.\t+\t0\tParent=CGI_10000012;\t0\r\n" ] } ], "prompt_number": 10 }, { "cell_type": "code", "collapsed": false, "input": [ "#wrong order " ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 12 }, { "cell_type": "markdown", "metadata": {}, "source": [ "#Summary Figures\n", "\n", "Details below.....\n", "\n", "\"BiGo_methratio_hist.key_17AC059E.png\"/\n", "\n", "\"BiGo_methratio_hist.key_17AC05EE.png\"/\n", "\n", "\n" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "--- \n", "###BiGo methratio intersect Exon" ] }, { "cell_type": "code", "collapsed": false, "input": [ "!intersectbed -a /Volumes/web/cnidarian/BiGo_methratio_boop_c.gff -b /Volumes/web/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_exon.gff > /Volumes/web/cnidarian/BiGo_methratio_boop_intersect_CDS_b.gff " ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 35 }, { "cell_type": "code", "collapsed": false, "input": [ "!wc /Volumes/web/cnidarian/BiGo_methratio_boop_intersect_CDS_b.gff" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ " 1028202 9253818 51391228 /Volumes/web/cnidarian/BiGo_methratio_boop_intersect_CDS_b.gff\r\n" ] } ], "prompt_number": 36 }, { "cell_type": "code", "collapsed": false, "input": [ "!head /Volumes/web/cnidarian/BiGo_methratio_boop_intersect_CDS_b.gff" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "C17212\tmethratio\tCpG\t165\t166\t0\t+\t.\t.\r", "\r\n", "C17212\tmethratio\tCpG\t169\t170\t0\t+\t.\t.\r", "\r\n", "C17212\tmethratio\tCpG\t234\t235\t0\t+\t.\t.\r", "\r\n", "C17212\tmethratio\tCpG\t249\t250\t0\t+\t.\t.\r", "\r\n", "C17316\tmethratio\tCpG\t45\t46\t0.125\t+\t.\t.\r", "\r\n", "C17316\tmethratio\tCpG\t71\t72\t0\t+\t.\t.\r", "\r\n", "C17316\tmethratio\tCpG\t74\t75\t0\t+\t.\t.\r", "\r\n", "C17316\tmethratio\tCpG\t89\t90\t0\t+\t.\t.\r", "\r\n", "C17316\tmethratio\tCpG\t101\t102\t0\t+\t.\t.\r", "\r\n", "C17316\tmethratio\tCpG\t208\t209\t0\t+\t.\t.\r", "\r\n" ] } ], "prompt_number": 37 }, { "cell_type": "code", "collapsed": false, "input": [ "from pandas import *\n", "\n", "# read data from data file into a pandas DataFrame \n", "CDSmr = read_table(\"/Volumes/web/cnidarian/BiGo_methratio_boop_intersect_CDS_b.gff\", # name of the data file\n", " #sep=\"\\t\", # what character separates each column?\n", " #na_values=[\"\", \" \"], # what values should be considered \"blank\" values?\n", " header=None)" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 38 }, { "cell_type": "code", "collapsed": false, "input": [ "CDSmr[5].hist(bins=50);\n", "#Axis limits are changed using the axis([xmin, xmax, ymin, ymax]) function.\n", "plt.axis([0, 1, 0, 150000]);\n", "plt.title('CDS');" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "display_data", "png": 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Ij49HbW3tTLtJREQzxM+SIiIKYfwsKSIimndYMMIEx2i9mIOKWaiYRWCwYBAR\nhYCp/lBSKOEcBhFRCJh6roJzGERENM+wYIQJjtF6MQcVs1Axi8BgwSAiIp9wDoOIKARwDoOIiMIG\nC0aY4BitF3NQMQsVswgMFgwiIvIJ5zCIiEIA5zCIiChssGCECY7RejEHFbNQMYvAYMEgIiKfcA6D\niCgEcA6DiIjCBgtGmOAYrRdzUDELVahkMdVHmIfax5hPZcZ/05uIiHwzONiH6YeQQhvnMIiI5oh/\nf5+bcxhERDTP+FUwXC4XHnroIdx3332wWCz4xS9+AQDo7e2F1WpFcnIy8vLy0N/fr2xTUVEBk8mE\n1NRUNDY2Ku0tLS1IS0uDyWTCzp07lfahoSEUFRXBZDIhOzsbFy9e9PcYI0KojNEGG3NQMQsVswgM\nvwqGRqPBz3/+c7S2tuLDDz/E66+/jr/85S+orKyE1WrFp59+itzcXFRWVgIA2tracOTIEbS1tcFm\ns2H79u3KJVFZWRmqqqrgcDjgcDhgs9kAAFVVVYiPj4fD4cDu3buxZ8+eAB0yERH5RQKgoKBAjh8/\nLikpKdLZ2SkiIh0dHZKSkiIiIvv375fKykrl+WvWrJEzZ85Ie3u7pKamKu2/+93v5Pvf/77ynA8/\n/FBERK5duyZ33nnnhO8LQIBuAWTc4z0xm1cG4tCIiALGe84af74afUy1zp9tpt+fv2b8LqkLFy7g\n448/RlZWFrq6uqDVagEAWq0WXV1dAID29nZkZ2cr2+j1eng8Hmg0Guj1eqVdp9PB4/EAADweDxIT\nEwEAUVFRWLx4MXp7exEXFzeuB+UAUr74OgZABgANAPUyNCcnh8tc5jKXQ2JZNbqcM64tZ9z6qZ7v\n6/5G/72AGZtJtRwcHJRvfvOb8vbbb4uISExMzJj1sbGxIiJSXl4uhw8fVtpLS0ulrq5OmpubZfXq\n1Up7U1OTrF+/XkRELBaLeDweZZ3BYJCenp4x+wevMBSnTp0KdhdCAnNQMQtVqGSBeX6F4fe7pK5d\nu4bCwkJs2rQJGzZsAOC9qujs7AQAdHR0YMmSJQC8Vw4ul0vZ1u12Q6/XQ6fTwe12T2gf3ebSpUsA\ngJGREQwMDExydUFERHPFr4IhIigtLYXZbMauXbuU9vz8fFRXVwMAqqurlUKSn5+P2tpaDA8Pw+l0\nwuFwIDMzEwkJCYiOjobdboeIoKamBgUFBRP2VVdXh9zc3Nvo4Tq0tX0w6d2U0dHhWXRGL3sjHXNQ\nMQsVswgdj1IBAAAH2ElEQVQMv27ce++99/Ctb30Ly5YtU25pr6ioQGZmJp544glcunQJSUlJeOut\ntxATEwMA2L9/Pw4ePIioqCi89tprWLNmDQDv22q3bNmCK1euYN26dcpbdIeGhrBp0yZ8/PHHiI+P\nR21tLZKSksZ2fsob96a/mcWPQyYimrH5fuNemN7pHXkF4/Tp0/wtCszhZsxCFSpZzPeCwTu9iYjI\nJ7zCICKaI7zCICIixXz/CPPpsGCEiYk3BUUm5qBiFqq5zEL9CPPJHvMbCwYREfmEcxhERAHk3zzF\ndOs4h0FERPMMC0aY4Hi1F3NQMQsVswgMFgwiIvIJ5zCIiAKIcxhERDTGVPdbhLMILBhRU95UM58/\nyZZjtF7MQcUsVLORxdT3W4SvGf/FvflnBFP9pw4OhvdvB0REMxGRcxic3yAiX0RHx31xJTGVuZlz\nCJU5jAi8wiAi8o067DSZyBuRiMA5jPDE8Wov5qBiFipmERgsGERE5BPOYYxbN4/jIKIpTDcXsWhR\nLC5f7p10Xaj8/QrOYRARzZHp5iIGBzVhf/9EoHBIaozJ79GYD/dncIzWK1RymO6P6MzVz9NXvrJo\nzvoQCsfrv9G32kfWPRX+YMEYY/IfnOnfVhcazp8/H+wuhIRQyWG6P6IzODg4xcn1/0x50p1u3VQn\n5CtX/p8fffCvH9Mf79Svn6kKzXRFZn4Xp/ktpAuGzWZDamoqTCYTXnrppSD2ZOq7w/15Ic+G/v7+\nOfteoWzPnv8b0BPhdOv8//+d6jfaa1O0T79uqpO/f33wtx/Tmfr1M1Whma6g+VOMKTBCdtL7+vXr\nSElJwYkTJ6DT6bBixQr87ne/w7333qs8ZzYmvQM76aSB94U5Wfu1abbxZ91CADfm4HuF+v6AwP7f\nT7duqv9ff/sRKj+3ofC9Qn1/c/m9OOl9S2fPnoXRaERSUhIAYOPGjaivrx9TMELfVB9Dwh/e2d3f\nXJn6Y2Yi8aYuCn8hWzA8Hg8SExOVZb1eD7vdPskz75xiD9O9YP1ZF+r7m8vvFWn7m8vvFer7m8vv\nFer7m8vvNRt9v30hWzB8GXcM0dE0IqKwFLKT3jqdDi6XS1l2uVzQ6/VB7BERUWQL2YKxfPlyOBwO\nXLhwAcPDwzhy5Ajy8/OD3S0ioogVskNSUVFR+NWvfoU1a9bg+vXrKC0tnWcT3kRE4SVkrzAA4OGH\nH8Zf//pX/OpXv0J1dfW092P88Ic/hMlkQnp6Oj7++OM57uncudW9Kb/5zW+Qnp6OZcuW4e///u/x\npz/9KQi9nBu+3qfz0UcfISoqCv/5n/85h72bW75kcfr0adx///2wWCzIycmZ2w7OoVtl0d3djbVr\n1yIjIwMWiwWHDh2a+07OgW3btkGr1SItLW3K59z2eVNC3MjIiBgMBnE6nTI8PCzp6enS1tY25jn/\n9V//JQ8//LCIiHz44YeSlZUVjK7OOl+y+OCDD6S/v19ERN59992IzmL0eQ899JD84z/+o9TV1QWh\np7PPlyz6+vrEbDaLy+USEZH/+Z//CUZXZ50vWTz77LPyox/9SES8OcTFxcm1a9eC0d1Z1dTUJOfO\nnROLxTLpen/OmyF9hQGMvR9Do9Eo92PcrKGhASUlJQCArKws9Pf3o6urKxjdnVW+ZPHggw9i8eLF\nALxZuN3uYHR11vmSBQD88pe/xGOPPYa77rorCL2cG75k8dvf/haFhYXKG0fuvHOqt6PPb75kcffd\nd+Py5csAgMuXLyM+Ph5RUSE7Ou+3VatWITY2dsr1/pw3Q75gTHY/hsfjueVzwvFE6UsWN6uqqsK6\ndevmomtzztefi/r6epSVlQHw7a3a85EvWTgcDvT29uKhhx7C8uXLUVNTM9fdnBO+ZPHkk0+itbUV\nS5cuRXp6Ol577bW57mZI8Oe8GfJl1dcXuYy7JyMcTw63c0ynTp3CwYMH8f77789ij4LHlyx27dqF\nyspKLFjg/SiE8T8j4cKXLK5du4Zz587h5MmT+Pzzz/Hggw8iOzsbJpNpDno4d3zJYv/+/cjIyMDp\n06fx2WefwWq14pNPPsGiRYvmoIeh5XbPmyFfMHy5H2P8c9xuN3Q63Zz1ca74em/Kn/70Jzz55JOw\n2WzTXpLOZ75k0dLSgo0bNwLwTnS+++670Gg0Yff2bF+ySExMxJ133ok77rgDd9xxB771rW/hk08+\nCbuC4UsWH3zwAX784x8DAAwGA77xjW/gr3/9K5YvXz6nfQ02v86bAZthmSXXrl2Te+65R5xOpwwN\nDd1y0vvMmTNhO9HrSxYXL14Ug8EgZ86cCVIv54YvWdxsy5Yt8h//8R9z2MO540sWf/nLXyQ3N1dG\nRkbkf//3f8VisUhra2uQejx7fMli9+7d8txzz4mISGdnp+h0Ounp6QlGd2ed0+n0adLb1/NmyF9h\nTHU/xr/+678CAL7//e9j3bp1eOedd2A0GvHVr34V//7v/x7kXs8OX7LYu3cv+vr6lHF7jUaDs2fP\nBrPbs8KXLCKFL1mkpqZi7dq1WLZsGRYuXIgnn3wSZrM5yD0PPF+yeOaZZ7B161akp6fjxo0bePnl\nlxEXF35/R6O4uBh/+MMf0N3djcTERDz//PO4ds37Cc/+njdD9uPNiYgotIT8u6SIiCg0sGAQEZFP\nWDCIiMgnLBhEROQTFgwiIvIJCwYREfnk/wM8TUjdvgEIwQAAAABJRU5ErkJggg==\n" } ], "prompt_number": 129 }, { "cell_type": "code", "collapsed": false, "input": [ "# pandas density plot\n", "CDSmr[5].plot(kind='kde', linewidth=3);\n", "plt.title('CDS')" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "pyout", "prompt_number": 70, "text": [ "" ] }, { "output_type": "display_data", "png": 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LzpbbFRXhvx7Z1yuvyPWpW24BrrtOu9fmjMA4DAQWFMyMQE1eW/k/s8slLiRG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\n" } ], "prompt_number": 70 }, { "cell_type": "markdown", "metadata": {}, "source": [ "--- \n", "###BiGo methratio intersect Promoter" ] }, { "cell_type": "code", "collapsed": false, "input": [ "!intersectbed -a /Volumes/web/cnidarian/BiGo_methratio_boop_c.gff -b /Volumes/web/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_1k5p_gene_promoter.gff > /Volumes/web/cnidarian/BiGo_methratio_boop_intersect_promoter.gff " ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 52 }, { "cell_type": "code", "collapsed": false, "input": [ "!head /Volumes/web/cnidarian/BiGo_methratio_boop_intersect_promoter.gff" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "C17476\tmethratio\tCpG\t291\t292\t0\t+\t.\t.\r", "\r\n", "C17476\tmethratio\tCpG\t389\t390\t0\t+\t.\t.\r", "\r\n", "C17476\tmethratio\tCpG\t391\t392\t0\t+\t.\t.\r", "\r\n", "C17476\tmethratio\tCpG\t398\t399\t0\t+\t.\t.\r", "\r\n", "C17476\tmethratio\tCpG\t414\t415\t0\t+\t.\t.\r", "\r\n", "C17476\tmethratio\tCpG\t439\t440\t0\t+\t.\t.\r", "\r\n", "C17476\tmethratio\tCpG\t455\t456\t0\t+\t.\t.\r", "\r\n", "C17476\tmethratio\tCpG\t460\t461\t0\t+\t.\t.\r", "\r\n", "C17476\tmethratio\tCpG\t469\t470\t0\t+\t.\t.\r", "\r\n", "C17998\tmethratio\tCpG\t424\t425\t0\t+\t.\t.\r", "\r\n" ] } ], "prompt_number": 53 }, { "cell_type": "code", "collapsed": false, "input": [ "from pandas import *\n", "\n", "# read data from data file into a pandas DataFrame \n", "Promr = read_table(\"/Volumes/web/cnidarian/BiGo_methratio_boop_intersect_promoter.gff\", # name of the data file\n", " #sep=\"\\t\", # what character separates each column?\n", " #na_values=[\"\", \" \"], # what values should be considered \"blank\" values?\n", " header=None)" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 54 }, { "cell_type": "code", "collapsed": false, "input": [ "Promr[5].hist(bins=50);\n", "#Axis limits are changed using the axis([xmin, xmax, ymin, ymax]) function.\n", "plt.axis([0, 1, 0, 20000]);\n", "plt.title('Promoter');" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "display_data", "png": 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} ], "prompt_number": 132 }, { "cell_type": "code", "collapsed": false, "input": [ "# pandas density plot\n", "Promr[5].plot(kind='kde', linewidth=3);\n", "plt.title('Promoter');" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "display_data", "png": 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BEUkxEehAR1NDrBHIi/Pa8mFfagcTgQ5Ib+0QEeH69TyPgIikmAh0oKNE4Gge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\ngIiok/t/Wv2fVMUVxVYAAAAASUVORK5CYII=\n" } ], "prompt_number": 139 }, { "cell_type": "markdown", "metadata": {}, "source": [ "--- \n", "###BiGo methratio intersect TE" ] }, { "cell_type": "code", "collapsed": false, "input": [ "!intersectbed -a /Volumes/web/cnidarian/BiGo_methratio_boop_c.gff -b /Volumes/web/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_TE.gff > /Volumes/web/cnidarian/BiGo_methratio_boop_intersect_TE.gff " ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 49 }, { "cell_type": "code", "collapsed": false, "input": [ "!head /Volumes/web/cnidarian/BiGo_methratio_boop_intersect_TE.gff" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "C10245\tmethratio\tCpG\t55\t56\t0\t+\t.\t.\r", "\r\n", "C10245\tmethratio\tCpG\t68\t69\t0\t+\t.\t.\r", "\r\n", "C11826\tmethratio\tCpG\t76\t77\t0.2\t+\t.\t.\r", "\r\n", "C11826\tmethratio\tCpG\t121\t122\t0.2\t+\t.\t.\r", "\r\n", "C11826\tmethratio\tCpG\t129\t130\t0.2\t+\t.\t.\r", "\r\n", "C11826\tmethratio\tCpG\t149\t150\t0.2\t+\t.\t.\r", "\r\n", "C11826\tmethratio\tCpG\t157\t158\t0.154\t+\t.\t.\r", "\r\n", "C13946\tmethratio\tCpG\t86\t87\t0\t+\t.\t.\r", "\r\n", "C13946\tmethratio\tCpG\t125\t126\t0\t+\t.\t.\r", "\r\n", "C13946\tmethratio\tCpG\t125\t126\t0\t+\t.\t.\r", "\r\n" ] } ], "prompt_number": 50 }, { "cell_type": "code", "collapsed": false, "input": [ "from pandas import *\n", "\n", "# read data from data file into a pandas DataFrame \n", "TEmr = read_table(\"/Volumes/web/cnidarian/BiGo_methratio_boop_intersect_TE.gff\", # name of the data file\n", " #sep=\"\\t\", # what character separates each column?\n", " #na_values=[\"\", \" \"], # what values should be considered \"blank\" values?\n", " header=None)" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 56 }, { "cell_type": "code", "collapsed": false, "input": [ "TEmr[5].hist(bins=50);\n", "#Axis limits are changed using the axis([xmin, xmax, ymin, ymax]) function.\n", "plt.axis([0, 1, 0, 15000]);\n", "plt.title('Transposable Elements');" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "display_data", "png": 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w/FTFWKgYCxVj4RxMDEREZIeJwYtw/FTFWKgYCxVj4RxMDEREZIeJwYtw/FTFWKgYCxVj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\nrFYrqqurMXv2bMyYMQNZWVm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} ], "prompt_number": 63 }, { "cell_type": "code", "collapsed": false, "input": [ "# pandas density plot\n", "TEmr[5].plot(kind='kde', linewidth=3);\n", "plt.title('Transposable Elements');" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "display_data", "png": 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} ], "prompt_number": 140 }, { "cell_type": "markdown", "metadata": {}, "source": [ "--- \n", "###BiGO methration intersect intron" ] }, { "cell_type": "code", "collapsed": false, "input": [ "!intersectbed -a /Volumes/web/cnidarian/BiGo_methratio_boop_c.gff -b /Volumes/web/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_intron.gff > /Volumes/web/cnidarian/BiGo_methratio_boop_intersect_intron.gff " ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 60 }, { "cell_type": "code", "collapsed": false, "input": [ "from pandas import *\n", "\n", "# read data from data file into a pandas DataFrame \n", "Intronmr = read_table(\"/Volumes/web/cnidarian/BiGo_methratio_boop_intersect_intron.gff\", # name of the data file\n", " #sep=\"\\t\", # what character separates each column?\n", " #na_values=[\"\", \" \"], # what values should be considered \"blank\" values?\n", " header=None)" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 61 }, { "cell_type": "code", "collapsed": false, "input": [ "Intronmr[5].hist(bins=50);\n", "#Axis limits are changed using the axis([xmin, xmax, ymin, ymax]) function.\n", "plt.axis([0, 1, 0, 150000]);\n", "plt.title('Intron');" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "display_data", "png": 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} ], "prompt_number": 136 }, { "cell_type": "code", "collapsed": false, "input": [ "# pandas density plot\n", "Intronmr[5].plot(kind='kde', linewidth=3);\n", "plt.title('Intron');" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "display_data", "png": 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gb/ly4N57gfPnxXZEBPDOO8C2bcB//mfzN0oymUxIShJBBBDpoY0ble8zNcVA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\n" } ], "prompt_number": 141 }, { "cell_type": "markdown", "metadata": {}, "source": [ "--- \n", "###BiGO methratio intersect 'other'" ] }, { "cell_type": "code", "collapsed": false, "input": [ "!intersectbed -a /Volumes/web/cnidarian/BiGo_methratio_boop_c.gff -b /Volumes/web/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_COMP_gene_prom_TE.bed > /Volumes/web/cnidarian/BiGo_methratio_boop_intersect_other.gff " ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 66 }, { "cell_type": "code", "collapsed": false, "input": [ "from pandas import *\n", "\n", "# read data from data file into a pandas DataFrame \n", "othermr = read_table(\"/Volumes/web/cnidarian/BiGo_methratio_boop_intersect_other.gff\", # name of the data file\n", " #sep=\"\\t\", # what character separates each column?\n", " #na_values=[\"\", \" \"], # what values should be considered \"blank\" values?\n", " header=None)" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 67 }, { "cell_type": "code", "collapsed": false, "input": [ "othermr[5].hist(bins=50);\n", "#Axis limits are changed using the axis([xmin, xmax, ymin, ymax]) function.\n", "plt.axis([0, 1, 0, 60000]);\n", "plt.title('Other');" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "display_data", "png": 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} ], "prompt_number": 138 }, { "cell_type": "code", "collapsed": false, "input": [ "# pandas density plot\n", "othermr[5].plot(kind='kde', linewidth=3);\n", "plt.title('Other');" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "display_data", "png": 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oLvYsbVL4xUW6A6QNdSJQrxWoqanpcRl/QYEyT/Bf/wW89poy6Qwol6vYskV5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\nAElFTkSuQmCC\n" } ], "prompt_number": 101 }, { "cell_type": "heading", "level": 2, "metadata": {}, "source": [ "Gene Level Methylation" ] }, { "cell_type": "code", "collapsed": false, "input": [ "#For each gene, need to get number of CG and Number of methylated CG \n", "#methylated CG defined as 5x 50%" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 1 }, { "cell_type": "code", "collapsed": false, "input": [ "#number of CGs per gene\n", "!intersectbed -c -a /Volumes/web/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_gene.gff -b /Volumes/web/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_CG.gff > /Volumes/web/cnidarian/TJGR_gene_CGcount.txt" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 2 }, { "cell_type": "code", "collapsed": false, "input": [ "!head /Volumes/web/cnidarian/TJGR_gene_CGcount.txt" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "C16582\tGLEAN\tmRNA\t35\t385\t0.555898\t-\t.\tID=CGI_10000001;\t14\r\n", "C17212\tGLEAN\tmRNA\t31\t363\t0.999572\t+\t.\tID=CGI_10000002;\t6\r\n", "C17316\tGLEAN\tmRNA\t30\t257\t0.555898\t+\t.\tID=CGI_10000003;\t10\r\n", "C17476\tGLEAN\tmRNA\t34\t257\t0.998947\t-\t.\tID=CGI_10000004;\t7\r\n", "C17998\tGLEAN\tmRNA\t196\t387\t1\t-\t.\tID=CGI_10000005;\t11\r\n", "C18346\tGLEAN\tmRNA\t174\t551\t1\t+\t.\tID=CGI_10000009;\t29\r\n", "C18428\tGLEAN\tmRNA\t286\t546\t0.555898\t-\t.\tID=CGI_10000010;\t24\r\n", "C18964\tGLEAN\tmRNA\t203\t658\t0.999572\t-\t.\tID=CGI_10000011;\t9\r\n", "C18980\tGLEAN\tmRNA\t30\t674\t0.555898\t+\t.\tID=CGI_10000012;\t56\r\n", "C19100\tGLEAN\tmRNA\t160\t681\t0.999955\t-\t.\tID=CGI_10000013;\t12\r\n" ] } ], "prompt_number": 3 }, { "cell_type": "code", "collapsed": false, "input": [ "!wc /Volumes/web/cnidarian/TJGR_gene_CGcount.txt" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ " 28027 280270 1915935 /Volumes/web/cnidarian/TJGR_gene_CGcount.txt\r\n" ] } ], "prompt_number": 6 }, { "cell_type": "code", "collapsed": false, "input": [ "#BiGO methylaiton file\n", "!head /Volumes/web/cnidarian/BiGo_methratio_mCG_tail.gff" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "C10093\tmethratio\tCpG\t107\t108\t1\t+\t.\t.\r", "\r\n", "C10137\tmethratio\tCpG\t18\t19\t0.733\t+\t.\t.\r", "\r\n", "C10137\tmethratio\tCpG\t30\t31\t0.778\t+\t.\t.\r", "\r\n", "C10137\tmethratio\tCpG\t39\t40\t0.783\t+\t.\t.\r", "\r\n", "C10137\tmethratio\tCpG\t72\t73\t0.524\t+\t.\t.\r", "\r\n", "C10137\tmethratio\tCpG\t81\t82\t0.692\t+\t.\t.\r", "\r\n", "C10137\tmethratio\tCpG\t97\t98\t0.556\t+\t.\t.\r", "\r\n", "C10311\tmethratio\tCpG\t56\t57\t1\t+\t.\t.\r", "\r\n", "C10671\tmethratio\tCpG\t22\t23\t0.5\t+\t.\t.\r", "\r\n", "C10671\tmethratio\tCpG\t152\t153\t0.5\t+\t.\t.\r", "\r\n" ] } ], "prompt_number": 41 }, { "cell_type": "code", "collapsed": false, "input": [ "!tail /Volumes/web/cnidarian/BiGo_methratio_mCG_tail.gff" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "scaffold999\tmethratio\tCpG\t58086\t58087\t0.733\t+\t.\t.\r", "\r\n", "scaffold999\tmethratio\tCpG\t90456\t90457\t0.6\t+\t.\t.\r", "\r\n", "scaffold999\tmethratio\tCpG\t90707\t90708\t0.6\t+\t.\t.\r", "\r\n", "scaffold999\tmethratio\tCpG\t90747\t90748\t0.559\t+\t.\t.\r", "\r\n", "scaffold999\tmethratio\tCpG\t91104\t91105\t0.5\t+\t.\t.\r", "\r\n", "scaffold999\tmethratio\tCpG\t91129\t91130\t0.579\t+\t.\t.\r", "\r\n", "scaffold999\tmethratio\tCpG\t92156\t92157\t0.514\t+\t.\t.\r", "\r\n", "scaffold999\tmethratio\tCpG\t100656\t100657\t0.5\t+\t.\t.\r", "\r\n", "scaffold999\tmethratio\tCpG\t100665\t100666\t0.6\t+\t.\t.\r", "\r\n", "scaffold999\tmethratio\tCpG\t148753\t148754\t0.882\t+\t.\t.\r", "\r\n" ] } ], "prompt_number": 42 }, { "cell_type": "code", "collapsed": false, "input": [ "#number of mCGs per gene\n", "!intersectbed -c -a /Volumes/web/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_gene.gff -b /Volumes/web/cnidarian/BiGo_methratio_mCG_tail.gff > /Volumes/web/cnidarian/BiGO_gene_mCGcount.txt" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 7 }, { "cell_type": "code", "collapsed": false, "input": [ "!head /Volumes/web/cnidarian/BiGO_gene_mCGcount.txt" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "C16582\tGLEAN\tmRNA\t35\t385\t0.555898\t-\t.\tID=CGI_10000001;\t0\r\n", "C17212\tGLEAN\tmRNA\t31\t363\t0.999572\t+\t.\tID=CGI_10000002;\t0\r\n", "C17316\tGLEAN\tmRNA\t30\t257\t0.555898\t+\t.\tID=CGI_10000003;\t0\r\n", "C17476\tGLEAN\tmRNA\t34\t257\t0.998947\t-\t.\tID=CGI_10000004;\t0\r\n", "C17998\tGLEAN\tmRNA\t196\t387\t1\t-\t.\tID=CGI_10000005;\t0\r\n", "C18346\tGLEAN\tmRNA\t174\t551\t1\t+\t.\tID=CGI_10000009;\t0\r\n", "C18428\tGLEAN\tmRNA\t286\t546\t0.555898\t-\t.\tID=CGI_10000010;\t0\r\n", "C18964\tGLEAN\tmRNA\t203\t658\t0.999572\t-\t.\tID=CGI_10000011;\t0\r\n", "C18980\tGLEAN\tmRNA\t30\t674\t0.555898\t+\t.\tID=CGI_10000012;\t0\r\n", "C19100\tGLEAN\tmRNA\t160\t681\t0.999955\t-\t.\tID=CGI_10000013;\t8\r\n" ] } ], "prompt_number": 8 }, { "cell_type": "code", "collapsed": false, "input": [ "!tail /Volumes/web/cnidarian/BiGO_gene_mCGcount.txt" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "scaffold22\tGLEAN\tmRNA\t1710615\t1726578\t0.998897\t+\t.\tID=CGI_10028929;\t59\r\n", "scaffold22\tGLEAN\tmRNA\t1728744\t1730768\t0.999999\t-\t.\tID=CGI_10028930;\t0\r\n", "scaffold22\tGLEAN\tmRNA\t1740746\t1762025\t0.648316\t+\t.\tID=CGI_10028931;\t175\r\n", "scaffold22\tGLEAN\tmRNA\t1748291\t1749451\t1\t-\t.\tID=CGI_10028932;\t11\r\n", "scaffold22\tGLEAN\tmRNA\t1763621\t1771882\t1\t+\t.\tID=CGI_10028933;\t46\r\n", "scaffold22\tGLEAN\tmRNA\t1784983\t1800181\t0.865666\t-\t.\tID=CGI_10028934;\t0\r\n", "scaffold22\tGLEAN\tmRNA\t1819528\t1821088\t0.988961\t+\t.\tID=CGI_10028935;\t0\r\n", "scaffold22\tGLEAN\tmRNA\t1863347\t1863687\t0.647996\t+\t.\tID=CGI_10028937;\t0\r\n", "scaffold22\tGLEAN\tmRNA\t1863760\t1864161\t0.544455\t+\t.\tID=CGI_10028938;\t0\r\n", "scaffold22\tGLEAN\tmRNA\t1869336\t1885890\t0.999933\t-\t.\tID=CGI_10028939;\t0\r\n" ] } ], "prompt_number": 39 }, { "cell_type": "code", "collapsed": false, "input": [ "!wc /Volumes/web/cnidarian/BiGO_gene_mCGcount.txt" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ " 28027 280270 1888975 /Volumes/web/cnidarian/BiGO_gene_mCGcount.txt\r\n" ] } ], "prompt_number": 40 }, { "cell_type": "code", "collapsed": false, "input": [ "#join \n", "#going for ugly excel cut and paste\n" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 43 }, { "cell_type": "code", "collapsed": false, "input": [ "#sneak peek at percent methylation per gene (when CG count >/= 10)\n" ], "language": "python", "metadata": {}, "outputs": [] }, { "cell_type": "markdown", "metadata": {}, "source": [ "\"Screenshot_9_13_13_7_56_AM_17E35F4D.png\"/" ] }, { "cell_type": "code", "collapsed": false, "input": [ "#only genes wiht >/= 10 cgs\n", "!head /Volumes/web/cnidarian/BiGo_gene_PerMeth.txt" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "GeneID\tCG\tmCG\tPercMeth\r\n", "CGI_10000309\t10\t10\t100\r\n", "CGI_10002318\t10\t10\t100\r\n", "CGI_10003667\t10\t10\t100\r\n", "CGI_10003855\t10\t10\t100\r\n", "CGI_10004087\t10\t10\t100\r\n", "CGI_10005035\t10\t10\t100\r\n", "CGI_10007691\t10\t10\t100\r\n", "CGI_10009829\t10\t10\t100\r\n", "CGI_10014371\t10\t10\t100\r\n" ] } ], "prompt_number": 45 }, { "cell_type": "code", "collapsed": false, "input": [ "#now need to examine percent methylation versus gene expression" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 44 }, { "cell_type": "markdown", "metadata": {}, "source": [ "sqlshare code to get expression\n", "```\n", "SELECT *\n", " FROM [sr320@washington.edu].[table_BiGo_gene_PerMeth.txt]gene\n", " left join\n", " [sr320@washington.edu].[BiGo_RNAseq_genes]exp\n", " on\n", " gene.\u200bGeneID = exp.[\"Feature ID\"]\u200b\u200b\u200b\u200b\u200b\u200b\u200b\u200b\u200b\n", "``` " ] }, { "cell_type": "code", "collapsed": false, "input": [ "!head /Volumes/web/cnidarian/BiGo_gene_pmeth_expression.csv" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "GeneID,CG,mCG,PercMeth,expression,genelength,uniquecount,totalcounts,rpkm\r\n", "CGI_10000001,14,0,0,15.319,351,0,14,15.319\r\n", "CGI_10000003,10,0,0,0,228,0,0,0\r\n", "CGI_10000005,11,0,0,0,192,0,0,0\r\n", "CGI_10000009,29,0,0,8.129,378,8,8,8.129\r\n", "CGI_10000010,24,0,0,103.009,261,0,70,103.009\r\n", "CGI_10000012,56,0,0,0.595,645,1,1,0.595\r\n", "CGI_10000014,21,0,0,338.241,243,0,214,338.241\r\n", "CGI_10000016,12,0,0,0,252,0,0,0\r\n", "CGI_10000017,14,0,0,0,447,0,0,0\r\n" ] } ], "prompt_number": 47 }, { "cell_type": "markdown", "metadata": {}, "source": [ "\"Screenshot_9_13_13_8_12_AM_17E36314.png\"/" ] }, { "cell_type": "heading", "level": 2, "metadata": {}, "source": [ "Promoter Methylation per gene" ] }, { "cell_type": "code", "collapsed": false, "input": [ "#will use promoter track that does not overlap genebodies\n", "!wc /Volumes/web/cnidarian/TJGR_prom_subtract_gene1.gff " ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ " 26706 240354 1803061 /Volumes/web/cnidarian/TJGR_prom_subtract_gene1.gff\r\n" ] } ], "prompt_number": 12 }, { "cell_type": "raw", "metadata": {}, "source": [ "#CG count per promoter\n", "!intersectbed -c -a /Volumes/web/cnidarian/TJGR_prom_subtract_gene1.gff -b /Volumes/web/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_CG.gff > /Volumes/web/cnidarian/TJGR_prom_subgene_CGcount.txt" ] }, { "cell_type": "code", "collapsed": false, "input": [ "!wc /Volumes/web/cnidarian/TJGR_prom_subgene_CGcount.txt" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ " 26706 267060 1877877 /Volumes/web/cnidarian/TJGR_prom_subgene_CGcount.txt\r\n" ] } ], "prompt_number": 17 }, { "cell_type": "code", "collapsed": false, "input": [ "#post tw/excel modding\n", "!head /Volumes/web/cnidarian/TJGR_prom_subgene_CGcount.txt" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "C16582\tflankbed\tpromoter\t386\t395\t.\t-\t.\tCGI_10000001\t0\r\n", "C17212\tflankbed\tpromoter\t1\t30\t.\t+\t.\tCGI_10000002\t0\r\n", "C17316\tflankbed\tpromoter\t1\t29\t.\t+\t.\tCGI_10000003\t0\r\n", "C17476\tflankbed\tpromoter\t258\t491\t.\t-\t.\tCGI_10000004\t10\r\n", "C17998\tflankbed\tpromoter\t388\t559\t.\t-\t.\tCGI_10000005\t8\r\n", "C18346\tflankbed\tpromoter\t1\t173\t.\t+\t.\tCGI_10000009\t21\r\n", "C18428\tflankbed\tpromoter\t547\t611\t.\t-\t.\tCGI_10000010\t2\r\n", "C18964\tflankbed\tpromoter\t659\t714\t.\t-\t.\tCGI_10000011\t2\r\n", "C18980\tflankbed\tpromoter\t1\t29\t.\t+\t.\tCGI_10000012\t5\r\n", "C19100\tflankbed\tpromoter\t682\t743\t.\t-\t.\tCGI_10000013\t2\r\n" ] } ], "prompt_number": 34 }, { "cell_type": "raw", "metadata": {}, "source": [ "#mCg per promoter\n", "!intersectbed -c -a /Volumes/web/cnidarian/TJGR_prom_subtract_gene1.gff -b /Volumes/web/cnidarian/BiGo_methratio_mCG_tail.gff > /Volumes/web/cnidarian/BiGo_prom_subgene_CGcount.txt" ] }, { "cell_type": "code", "collapsed": false, "input": [ "!head /Volumes/web/cnidarian/BiGo_prom_subgene_CGcount.txt" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "C16582\tflankbed\tpromoter\t386\t395\t.\t-\t.\tID=CGI_10000001;\r", "\t0\r\n", "C17212\tflankbed\tpromoter\t1\t30\t.\t+\t.\tID=CGI_10000002;\r", "\t0\r\n", "C17316\tflankbed\tpromoter\t1\t29\t.\t+\t.\tID=CGI_10000003;\r", "\t0\r\n", "C17476\tflankbed\tpromoter\t258\t491\t.\t-\t.\tID=CGI_10000004;\r", "\t0\r\n", "C17998\tflankbed\tpromoter\t388\t559\t.\t-\t.\tID=CGI_10000005;\r", "\t0\r\n", "C18346\tflankbed\tpromoter\t1\t173\t.\t+\t.\tID=CGI_10000009;\r", "\t0\r\n", "C18428\tflankbed\tpromoter\t547\t611\t.\t-\t.\tID=CGI_10000010;\r", "\t0\r\n", "C18964\tflankbed\tpromoter\t659\t714\t.\t-\t.\tID=CGI_10000011;\r", "\t0\r\n", "C18980\tflankbed\tpromoter\t1\t29\t.\t+\t.\tID=CGI_10000012;\r", "\t0\r\n", "C19100\tflankbed\tpromoter\t682\t743\t.\t-\t.\tID=CGI_10000013;\r", "\t0\r\n" ] } ], "prompt_number": 16 }, { "cell_type": "markdown", "metadata": {}, "source": [ "crazy line skip issue \n", "\"eagle.fish.washington.edu_cnidarian_BiGo_prom_subgene_CGcount.txt_17E2745E.png\"/" ] }, { "cell_type": "code", "collapsed": false, "input": [ "#post tw/excel modding\n", "!head /Volumes/web/cnidarian/BiGo_prom_subgene_mCGcount.txt" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "C16582\tflankbed\tpromoter\t386\t395\t.\t-\t.\tCGI_10000001\t0\r\n", "C17212\tflankbed\tpromoter\t1\t30\t.\t+\t.\tCGI_10000002\t0\r\n", "C17316\tflankbed\tpromoter\t1\t29\t.\t+\t.\tCGI_10000003\t0\r\n", "C17476\tflankbed\tpromoter\t258\t491\t.\t-\t.\tCGI_10000004\t0\r\n", "C17998\tflankbed\tpromoter\t388\t559\t.\t-\t.\tCGI_10000005\t0\r\n", "C18346\tflankbed\tpromoter\t1\t173\t.\t+\t.\tCGI_10000009\t0\r\n", "C18428\tflankbed\tpromoter\t547\t611\t.\t-\t.\tCGI_10000010\t0\r\n", "C18964\tflankbed\tpromoter\t659\t714\t.\t-\t.\tCGI_10000011\t0\r\n", "C18980\tflankbed\tpromoter\t1\t29\t.\t+\t.\tCGI_10000012\t0\r\n", "C19100\tflankbed\tpromoter\t682\t743\t.\t-\t.\tCGI_10000013\t0\r\n" ] } ], "prompt_number": 35 }, { "cell_type": "markdown", "metadata": {}, "source": [ "In SQLSHare\n", "\n", "Very close \n", "\n", "\n", "\"SQLShare_-_View_Query_17E351B7.png\"/\n", "\n", "```\n", "SELECT \n", " p.Column9 as GeneID,\n", " p.Column10 as CGcount,\n", " m.Column10 as mCGcount,\n", " Case when p.Column10 = '0'\n", " then m.Column10\n", " Else (m.Column10/p.Column10)\n", " END as PerMeth\n", " \n", " FROM [sr320@washington.edu].[TJGR_prom_subgene_CGcount.txt]p\n", "LEFT Join\n", " [sr320@washington.edu].[BiGo_prom_subgene_mCGcount.txt]m\n", "on\n", " p.Column9 = m.Column9\n", "``` " ] }, { "cell_type": "code", "collapsed": false, "input": [ "#give up into EXcel\n", "!head /Volumes/web/cnidarian/BiGo_prom_subgene_PerMeth.txt" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "GeneID\tCGcount\tmCGcount\tPmeth\r\n", "CGI_10001604\t10\t10\t100\r\n", "CGI_10020784\t10\t10\t100\r\n", "CGI_10021695\t10\t10\t100\r\n", "CGI_10021827\t10\t10\t100\r\n", "CGI_10021844\t10\t10\t100\r\n", "CGI_10021960\t10\t10\t100\r\n", "CGI_10011876\t10\t10\t100\r\n", "CGI_10009511\t10\t10\t100\r\n", "CGI_10006768\t10\t10\t100\r\n" ] } ], "prompt_number": 37 }, { "cell_type": "markdown", "metadata": {}, "source": [ "code \n", "```\n", "SELECT *\n", " FROM [sr320@washington.edu].[BiGo_prom_subgene_PerMeth.txt]pr\n", " left join\n", " [sr320@washington.edu].[BiGo_RNAseq_genes]exp\n", " on\n", " pr.\u200bGeneID = exp.[\"Feature ID\"]\n", "``` \n", " " ] }, { "cell_type": "code", "collapsed": false, "input": [ "#file manipulated in excel\n", "!head /Volumes/web/cnidarian/BiGo_prom_subgene_pmeth_expression.txt" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "GeneID\tCGcount\tmCGcount\tPmeth\tExp\r\n", "CGI_10012330\t27\t0\t0\t35637.269\r\n", "CGI_10001766\t21\t0\t0\t19885.868\r\n", "CGI_10021069\t19\t0\t0\t17576.275\r\n", "CGI_10012474\t15\t1\t6.666666667\t13030.698\r\n", "CGI_10014767\t42\t0\t0\t12227.203\r\n", "CGI_10026412\t30\t0\t0\t10903.164\r\n", "CGI_10008493\t18\t1\t5.555555556\t10023.721\r\n", "CGI_10024065\t26\t0\t0\t9939.849\r\n", "CGI_10012002\t13\t9\t69.23076923\t9554.514\r\n" ] } ], "prompt_number": 1 }, { "cell_type": "markdown", "metadata": {}, "source": [ "\"Screenshot_9_13_13_7_30_AM_17E3598F.png\"/" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "\"untitled__1_.csv_17E35B41.png\"/" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "\"Screenshot_9_13_13_8_58_AM_17E36E27.png\"/" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Closeup with random\n", "\n", "\"Screenshot_9_13_13_9_08_AM_17E36FED.png\"/mm" ] }, { "cell_type": "heading", "level": 2, "metadata": {}, "source": [ "Promoter with CpG Islands methylation" ] }, { "cell_type": "code", "collapsed": false, "input": [], "language": "python", "metadata": {}, "outputs": [] }, { "cell_type": "raw", "metadata": {}, "source": [ "Given that only \"promoters\" with islands are examined - an absolute methylation approach could be used" ] }, { "cell_type": "code", "collapsed": false, "input": [ "#absolute methylation\n", "#using the conserved model\n", "#Window size [100]: \n", "#Minimum length of an island [200]: \n", "#Minimum observed/expected [0.6]: \n", "#Minimum percentage [50.]: 45\n", "#promoter does not overlap gene\n", "!intersectbed -c -a /Volumes/web/cnidarian/TJGR_prom_notgene_cpgIsland1u.gff -b /Volumes/web/cnidarian/BiGo_methratio_mCG_tail.gff > /Volumes/web/cnidarian/BiGo_pro_island1u_intersect_mCpG.txt" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 19 }, { "cell_type": "code", "collapsed": false, "input": [ "!head /Volumes/web/cnidarian/BiGo_pro_island1u_intersect_mCpG.txt" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "C18346\tflankbed\tpromoter\t1\t173\t.\t+\t.\tCGI_10000009\t0\r\n", "C18428\tflankbed\tpromoter\t547\t611\t.\t-\t.\tCGI_10000010\t0\r\n", "C19356\tflankbed\tpromoter\t1\t354\t.\t+\t.\tCGI_10000014\t0\r\n", "C19532\tflankbed\tpromoter\t602\t843\t.\t-\t.\tCGI_10000017\t0\r\n", "C20578\tflankbed\tpromoter\t1\t698\t.\t+\t.\tCGI_10000034\t0\r\n", "C21046\tflankbed\tpromoter\t813\t1275\t.\t-\t.\tCGI_10000042\t0\r\n", "C21254\tflankbed\tpromoter\t1\t669\t.\t+\t.\tCGI_10000047\t0\r\n", "C21260\tflankbed\tpromoter\t1176\t1343\t.\t-\t.\tCGI_10000048\t0\r\n", "C22036\tflankbed\tpromoter\t1\t947\t.\t+\t.\tCGI_10000068\t0\r\n", "C22346\tflankbed\tpromoter\t756\t1755\t.\t-\t.\tCGI_10000079\t0\r\n" ] } ], "prompt_number": 49 }, { "cell_type": "code", "collapsed": false, "input": [ "!wc /Volumes/web/cnidarian/BiGo_pro_island1u_intersect_mCpG.txt" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ " 2464 24640 170901 /Volumes/web/cnidarian/BiGo_pro_island1u_intersect_mCpG.txt\r\n" ] } ], "prompt_number": 21 }, { "cell_type": "code", "collapsed": false, "input": [ "!intersectbed -c -a /Volumes/web/cnidarian/TJGR_prom_notgene_cpgIsland1u.gff -b /Volumes/web/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_CG.gff > /Volumes/web/cnidarian/TJGR_pro_island1u_intersect_CpG.txt" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 29 }, { "cell_type": "code", "collapsed": false, "input": [ "!wc /Volumes/web/cnidarian/TJGR_pro_island1u_intersect_CpG.txt" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ " 2464 24640 173098 /Volumes/web/cnidarian/TJGR_pro_island1u_intersect_CpG.txt\r\n" ] } ], "prompt_number": 30 }, { "cell_type": "code", "collapsed": false, "input": [ "#geneexprssion level \n", "!head /Volumes/web/cnidarian/BiGo_RNAseq_genes" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "\"Feature ID\"\t\"Expression values\"\t\"Gene length\"\t\"Unique gene reads\"\t\"Total gene reads\"\t\"RPKM\"\r\n", "CGI_10000780\t0\t1350\t0\t0\t0\r\n", "CGI_10000456\t7.892\t438\t8\t9\t7.892\r\n", "CGI_10000457\t7.643\t603\t6\t12\t7.643\r\n", "CGI_10000774\t0\t375\t0\t0\t0\r\n", "CGI_10000917\t0\t426\t0\t0\t0\r\n", "CGI_10000861\t0\t2004\t0\t0\t0\r\n", "CGI_10000994\t16.913\t1635\t64\t72\t16.913\r\n", "CGI_10000643\t0.696\t552\t1\t1\t0.696\r\n", "CGI_10000763\t0\t249\t0\t0\t0\r\n" ] } ], "prompt_number": 31 }, { "cell_type": "code", "collapsed": false, "input": [ "#lets plot absolute methylation versus expression\n" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 32 }, { "cell_type": "code", "collapsed": false, "input": [ "#simpled up methylation file\n", "!wc /Volumes/web/cnidarian/BiGo_pro_island1u_intersect_mCpG_slm.csv\n" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ " 0 2464 37020 /Volumes/web/cnidarian/BiGo_pro_island1u_intersect_mCpG_slm.csv\r\n" ] } ], "prompt_number": 54 }, { "cell_type": "markdown", "metadata": {}, "source": [ "code\n", "```\n", "SELECT *\n", " FROM [sr320@washington.edu].[table_BiGo_pro_island1u_intersect_mCpG_slm.csv]pr_is\n", " left join\n", " [sr320@washington.edu].[BiGo_RNAseq_genes]exp\n", " on\n", " pr_is.Column1 = exp.[\"Feature ID\"]\u200b\n", "``` " ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "\"Screenshot_9_13_13_9_39_AM_17E3772C.png\"/" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "\"Screenshot_9_13_13_9_43_AM_17E3786E.png\"/" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "\"Screenshot_9_13_13_9_40_AM_17E37780.png\"/" ] }, { "cell_type": "code", "collapsed": false, "input": [], "language": "python", "metadata": {}, "outputs": [] } ], "metadata": {} } ] }