{ "metadata": { "name": "", "signature": "sha256:b6be0fdc44d91775dd90b15c69e5c16e0cd65505e4d6388ad78ca04cce63b921" }, "nbformat": 3, "nbformat_minor": 0, "worksheets": [ { "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "Method 3: (species(super-bin) based + error correction)\n", "====\n", "\n", "- Based on samples-by-super-bin matrix. \n", "- should use all the reads instead of the high coverage reads in the first two methods\n", "- error correction using correc_error python script\n", "\n", "\n", "Result\n", "----\n", "- worst: no significant separation.\n", "- not expected.\n", "- according to improvement in methods, should get better separation\n", "- possible reason:\n", " - error correction does not work well\n", " - using all the reads including low coverage introduce noise?\n", " " ] }, { "cell_type": "code", "collapsed": false, "input": [ "import pandas as pd\n", "import numpy as np\n", "import scipy\n", "from IPython.display import HTML\n", "from scipy.cluster.hierarchy import linkage, dendrogram\n", "from scipy.spatial.distance import pdist, squareform\n", "from IPython.display import Image\n", "from pandas import *" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 33 }, { "cell_type": "code", "collapsed": false, "input": [ "GOS=pd.read_csv('../data/matrix_species.out',delimiter=' ',header=None)\n" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 34 }, { "cell_type": "code", "collapsed": false, "input": [ "#label=pd.read_csv('../data/config-GOS.txt',delimiter=' ',header=None)\n", "pre_label = GOS.iloc[:,0].tolist()\n", "label = []\n", "for stuff in pre_label:\n", " print stuff\n", " label.append(str(stuff).split(\".trimmed.\")[0])\n", "len(label)\n", "print label\n", "GOS" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "O2.UC-11.trimmed.fa.clippered.corr.comb\n", "O2.UC-12.trimmed.fa.clippered.corr.comb\n", "O2.UC-13.trimmed.fa.clippered.corr.comb\n", "O2.UC-14.trimmed.fa.clippered.corr.comb\n", "O2.UC-16.trimmed.fa.clippered.corr.comb\n", "O2.UC-17.trimmed.fa.clippered.corr.comb\n", "O2.UC-18.trimmed.fa.clippered.corr.comb\n", "O2.UC-19.trimmed.fa.clippered.corr.comb\n", "O2.UC-1.trimmed.fa.clippered.corr.comb\n", "O2.UC-20.trimmed.fa.clippered.corr.comb\n", "O2.UC-21.trimmed.fa.clippered.corr.comb\n", "O2.UC-22.trimmed.fa.clippered.corr.comb\n", "O2.UC-23.trimmed.fa.clippered.corr.comb\n", "O2.UC-24.trimmed.fa.clippered.corr.comb\n", "O2.UC-4.trimmed.fa.clippered.corr.comb\n", "V1.CD-11.trimmed.fa.clippered.corr.comb\n", "V1.CD-12.trimmed.fa.clippered.corr.comb\n", "V1.CD-13.trimmed.fa.clippered.corr.comb\n", "V1.CD-14.trimmed.fa.clippered.corr.comb\n", "V1.CD-15.trimmed.fa.clippered.corr.comb\n", "V1.CD-1.trimmed.fa.clippered.corr.comb\n", "V1.CD-2.trimmed.fa.clippered.corr.comb\n", "V1.CD-3.trimmed.fa.clippered.corr.comb\n", "V1.CD-4.trimmed.fa.clippered.corr.comb\n", "V1.CD-6.trimmed.fa.clippered.corr.comb\n", "V1.CD-8.trimmed.fa.clippered.corr.comb\n", "V1.CD-9.trimmed.fa.clippered.corr.comb\n", "V1.UC-10.trimmed.fa.clippered.corr.comb\n", "V1.UC-13.trimmed.fa.clippered.corr.comb\n", "V1.UC-14.trimmed.fa.clippered.corr.comb\n", "V1.UC-15.trimmed.fa.clippered.corr.comb\n", "V1.UC-17.trimmed.fa.clippered.corr.comb\n", "V1.UC-18.trimmed.fa.clippered.corr.comb\n", "V1.UC-19.trimmed.fa.clippered.corr.comb\n", "V1.UC-21.trimmed.fa.clippered.corr.comb\n", "V1.UC-6.trimmed.fa.clippered.corr.comb\n", "V1.UC-7.trimmed.fa.clippered.corr.comb\n", "V1.UC-8.trimmed.fa.clippered.corr.comb\n", "V1.UC-9.trimmed.fa.clippered.corr.comb\n", "['O2.UC-11', 'O2.UC-12', 'O2.UC-13', 'O2.UC-14', 'O2.UC-16', 'O2.UC-17', 'O2.UC-18', 'O2.UC-19', 'O2.UC-1', 'O2.UC-20', 'O2.UC-21', 'O2.UC-22', 'O2.UC-23', 'O2.UC-24', 'O2.UC-4', 'V1.CD-11', 'V1.CD-12', 'V1.CD-13', 'V1.CD-14', 'V1.CD-15', 'V1.CD-1', 'V1.CD-2', 'V1.CD-3', 'V1.CD-4', 'V1.CD-6', 'V1.CD-8', 'V1.CD-9', 'V1.UC-10', 'V1.UC-13', 'V1.UC-14', 'V1.UC-15', 'V1.UC-17', 'V1.UC-18', 'V1.UC-19', 'V1.UC-21', 'V1.UC-6', 'V1.UC-7', 'V1.UC-8', 'V1.UC-9']\n" ] }, { "html": [ "
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30 | \n", "V1.UC-15.trimmed.fa.clippered.corr.comb | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "... | \n", "0.975791 | \n", "0.000000 | \n", "0.980196 | \n", "0.976490 | \n", "0.986267 | \n", "0.987606 | \n", "0.985863 | \n", "0.984048 | \n", "0.970740 | \n", "0.956262 | \n", "
31 | \n", "V1.UC-17.trimmed.fa.clippered.corr.comb | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "... | \n", "0.967284 | \n", "0.980196 | \n", "0.000000 | \n", "0.980102 | \n", "0.986288 | \n", "0.984708 | \n", "0.967099 | \n", "0.983253 | \n", "0.981986 | \n", "0.961695 | \n", "
32 | \n", "V1.UC-18.trimmed.fa.clippered.corr.comb | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "... | \n", "0.985336 | \n", "0.976490 | \n", "0.980102 | \n", "0.000000 | \n", "0.983417 | \n", "0.987396 | \n", "0.963790 | \n", "0.984856 | \n", "0.973331 | \n", "0.985179 | \n", "
33 | \n", "V1.UC-19.trimmed.fa.clippered.corr.comb | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "... | \n", "0.990910 | \n", "0.986267 | \n", "0.986288 | \n", "0.983417 | \n", "0.000000 | \n", "0.991847 | \n", "0.987864 | \n", "0.991273 | \n", "0.986927 | \n", "0.982452 | \n", "
34 | \n", "V1.UC-21.trimmed.fa.clippered.corr.comb | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "... | \n", "0.986948 | \n", "0.987606 | \n", "0.984708 | \n", "0.987396 | \n", "0.991847 | \n", "0.000000 | \n", "0.989299 | \n", "0.985895 | \n", "0.984929 | \n", "0.985725 | \n", "
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36 | \n", "V1.UC-7.trimmed.fa.clippered.corr.comb | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "... | \n", "0.971271 | \n", "0.984048 | \n", "0.983253 | \n", "0.984856 | \n", "0.991273 | \n", "0.985895 | \n", "0.974708 | \n", "0.000000 | \n", "0.973391 | \n", "0.974878 | \n", "
37 | \n", "V1.UC-8.trimmed.fa.clippered.corr.comb | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "... | \n", "0.955809 | \n", "0.970740 | \n", "0.981986 | \n", "0.973331 | \n", "0.986927 | \n", "0.984929 | \n", "0.964166 | \n", "0.973391 | \n", "0.000000 | \n", "0.966591 | \n", "
38 | \n", "V1.UC-9.trimmed.fa.clippered.corr.comb | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "... | \n", "0.971796 | \n", "0.956262 | \n", "0.961695 | \n", "0.985179 | \n", "0.982452 | \n", "0.985725 | \n", "0.973366 | \n", "0.974878 | \n", "0.966591 | \n", "0.000000 | \n", "
39 rows \u00d7 40 columns
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12 | \n", "0.984447 | \n", "0.972965 | \n", "0.980964 | \n", "0.988268 | \n", "0.994213 | \n", "0.988335 | \n", "0.986989 | \n", "0.968038 | \n", "0.980521 | \n", "0.954648 | \n", "... | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "
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15 | \n", "0.989466 | \n", "0.994130 | \n", "0.987616 | \n", "0.989969 | \n", "0.997060 | \n", "0.986563 | \n", "0.986087 | \n", "0.991634 | \n", "0.995343 | \n", "0.986433 | \n", "... | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "
16 | \n", "0.995049 | \n", "0.991574 | \n", "0.994829 | \n", "0.983964 | \n", "0.997119 | \n", "0.989323 | \n", "0.956587 | \n", "0.983880 | \n", "0.992616 | \n", "0.976638 | \n", "... | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "
17 | \n", "0.946449 | \n", "0.947449 | \n", "0.971230 | \n", "0.981234 | \n", "0.985573 | \n", "0.985884 | \n", "0.982174 | \n", "0.960176 | \n", "0.978126 | \n", "0.959651 | \n", "... | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "
18 | \n", "0.980329 | \n", "0.966711 | \n", "0.974045 | \n", "0.976920 | \n", "0.992546 | \n", "0.981639 | \n", "0.988111 | \n", "0.958290 | \n", "0.969359 | \n", "0.961448 | \n", "... | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "
19 | \n", "0.940929 | \n", "0.979535 | \n", "0.981849 | \n", "0.983622 | \n", "0.995719 | \n", "0.977142 | \n", "0.981263 | \n", "0.969507 | \n", "0.986944 | \n", "0.944355 | \n", "... | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "
20 | \n", "0.993891 | \n", "0.988433 | \n", "0.988552 | \n", "0.984780 | \n", "0.996230 | \n", "0.977126 | \n", "0.986633 | \n", "0.986580 | \n", "0.994292 | \n", "0.975247 | \n", "... | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "
21 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "... | \n", "0.966567 | \n", "0.958694 | \n", "0.972513 | \n", "0.984443 | \n", "0.990661 | \n", "0.984929 | \n", "0.979776 | \n", "0.976809 | \n", "0.968202 | \n", "0.951865 | \n", "
22 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "1.000000 | \n", "... | \n", "0.960166 | \n", "0.969740 | \n", "0.951027 | \n", "0.968895 | \n", "0.991520 | \n", "0.992930 | \n", "0.930383 | \n", "0.982502 | \n", "0.955651 | \n", "0.960562 | \n", "
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39 rows \u00d7 39 columns
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