{ "metadata": { "name": "Methylkit_Formatting_AdapterTrimmed" }, "nbformat": 3, "nbformat_minor": 0, "worksheets": [ { "cells": [ { "cell_type": "heading", "level": 3, "metadata": {}, "source": "Create a file formatted for visualization in the R package methylKit" }, { "cell_type": "heading", "level": 3, "metadata": {}, "source": "M1" }, { "cell_type": "code", "collapsed": false, "input": "!awk '{print $1,$2,$2+1,$3,$8,($7/$8),(1-($7/$8))}' /Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/methylkit_out_M1.txt ", "language": "python", "metadata": {}, "outputs": [], "prompt_number": 3 }, { "cell_type": "code", "collapsed": false, "input": "#Second line of code for creating a formatted file for methylKit\n!tr ' ' \"\\t\" /Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/methylKit/methylkit_out_M1final.txt", "language": "python", "metadata": {}, "outputs": [], "prompt_number": 4 }, { "cell_type": "code", "collapsed": false, "input": "!head 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creating a formatted file for methylKit\n!tr ' ' \"\\t\" /Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/methylKit/methylkit_out_M3final.txt", "language": "python", "metadata": {}, "outputs": [], "prompt_number": 7 }, { "cell_type": "code", "collapsed": false, "input": "!head /Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/methylKit/methylkit_out_M3final.txt", "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": "C13128\t87\t88\t+\t5\t0\t1\r\nC13208\t83\t84\t+\t7\t0.428571\t0.571429\r\nC13220\t164\t165\t+\t6\t0\t1\r\nC13442\t65\t66\t+\t5\t0\t1\r\nC13442\t79\t80\t+\t5\t0\t1\r\nC13612\t89\t90\t+\t5\t0\t1\r\nC13992\t54\t55\t+\t5\t0\t1\r\nC14180\t158\t159\t+\t5\t0\t1\r\nC14220\t96\t97\t+\t12\t0\t1\r\nC14220\t143\t144\t+\t7\t0\t1\r\n" } ], "prompt_number": 8 }, { "cell_type": "heading", "level": 3, "metadata": {}, "source": "T1D3" }, { "cell_type": "code", "collapsed": false, "input": "!awk '{print 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"T3D5" }, { "cell_type": "code", "collapsed": false, "input": "!awk '{print $1,$2,$2+1,$3,$8,($7/$8),(1-($7/$8))}' /Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/methylkit_out_T3D5.txt ", "language": "python", "metadata": {}, "outputs": [], "prompt_number": 18 }, { "cell_type": "code", "collapsed": false, "input": "#Second line of code for creating a formatted file for methylKit\n!tr ' ' \"\\t\" /Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/methylKit/methylkit_out_T3D5final.txt", "language": "python", "metadata": {}, "outputs": [], "prompt_number": 19 }, { "cell_type": "code", "collapsed": false, "input": "!head /Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/methylKit/methylkit_out_T3D5final.txt", "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": "C13220\t164\t165\t+\t5\t0\t1\r\nC13490\t83\t84\t+\t5\t0\t1\r\nC13546\t84\t85\t+\t8\t0\t1\r\nC14220\t96\t97\t+\t5\t0\t1\r\nC14220\t143\t144\t+\t5\t0\t1\r\nC14450\t60\t61\t+\t6\t0\t1\r\nC14450\t94\t95\t+\t5\t0\t1\r\nC14450\t106\t107\t+\t6\t0\t1\r\nC14450\t118\t119\t+\t5\t0\t1\r\nC14450\t187\t188\t+\t6\t0.166667\t0.833333\r\n" } ], "prompt_number": 20 }, { "cell_type": "code", "collapsed": false, "input": "#NOTEBOOK NAME\nnb='Methylkit_Formatting_AdapterTrimmed'\n\n#NOTEBOOK LOCATION\nnbloc='/Users/claireolson/Dropbox/Lab\\ \\(1\\)/IPython_nbs/Claire/'\n\n\n\n#TIMESTAMP\ndate=!date +%m%d_%H%M\n#LOCATION OF POST DIRECTORY\npost='/Volumes/web/Mollusk/iPython_Posts/'", "language": "python", "metadata": {}, "outputs": [], "prompt_number": 21 }, { "cell_type": "code", "collapsed": false, "input": "cd {post}", "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": "/Volumes/web/Mollusk/iPython_Posts\n" } ], "prompt_number": 22 }, { "cell_type": "code", "collapsed": false, "input": "!ipython nbconvert {nbloc}{nb} --to html --template full --output {nb}{date}", "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": "[NbConvertApp] Using existing profile dir: u'/Users/claireolson/.ipython/profile_default'\r\n" }, { "output_type": "stream", "stream": "stdout", "text": "[NbConvertApp] Converting notebook /Users/claireolson/Dropbox/Lab (1)/IPython_nbs/Claire/Methylkit_Formatting_AdapterTrimmed.ipynb to html\r\n[NbConvertApp] Support files will be in Methylkit_Formatting_AdapterTrimmed[0408_1324]_files/\r\n" }, { "output_type": "stream", "stream": "stdout", "text": "[NbConvertApp] Loaded template html_full.tpl\r\n" }, { "output_type": "stream", "stream": "stdout", "text": "[NbConvertApp] Writing 208694 bytes to Methylkit_Formatting_AdapterTrimmed[0408_1324].html\r\n" } ], "prompt_number": 23 }, { "cell_type": "code", "collapsed": false, "input": "", "language": "python", "metadata": {}, "outputs": [] } ], "metadata": {} } ] }