{ "metadata": { "name": "", "signature": "sha256:f11711f38fbbed7cb8cfa1a375d8014b3df45dd7fa4f1e7ae5356ab8c9ec1ad4" }, "nbformat": 3, "nbformat_minor": 0, "worksheets": [ { "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "## Looking at Qi method\n", "\n", "In the repository from the Qi experiment there is a file which it appears is used to extract the features:" ] }, { "cell_type": "code", "collapsed": false, "input": [ "cd 1gene-expression/" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "/home/gavin/Documents/MRes/YeastPPI-shared-08/1gene-expression\n" ] } ], "prompt_number": 1 }, { "cell_type": "code", "collapsed": false, "input": [ "ls" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "\u001b[0m\u001b[40m\u001b[m\u001b[00mall_expression_fixed_s4_csv.txt\u001b[0m \u001b[40m\u001b[m\u001b[00mget_gene_expression_summary.pl\u001b[0m\r\n", "\u001b[40m\u001b[m\u001b[00mexpressionYanjunSplit.txt\u001b[0m \u001b[40m\u001b[m\u001b[00mYeastGeneListOrfGeneName-106_pval_v9.0.txt\u001b[0m\r\n", "\u001b[40m\u001b[m\u001b[00mget_gene_expression.pl\u001b[0m\r\n" ] } ], "prompt_number": 2 }, { "cell_type": "markdown", "metadata": {}, "source": [ "Using pandas to read in the large csv." ] }, { "cell_type": "code", "collapsed": false, "input": [ "import pandas as pd\n", "d = pd.read_csv(\"all_expression_fixed_s4_csv.txt\", header=None)" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 3 }, { "cell_type": "code", "collapsed": false, "input": [ "d.head()" ], "language": "python", "metadata": {}, "outputs": [ { "html": [ "
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