{ "metadata": { "name": "Filtering_Larvae_AdapterTrimmed" }, "nbformat": 3, "nbformat_minor": 0, "worksheets": [ { "cells": [ { "cell_type": "heading", "level": 3, "metadata": {}, "source": "Filtering larvae files that have been trimmed for adapters for context and coverage" }, { "cell_type": "heading", "level": 3, "metadata": {}, "source": "M1" }, { "cell_type": "code", "collapsed": false, "input": "#Output for methratio file\nmethratio=\"/Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_methratio_files/\"\n\n#Location of filtered files\nfiltered=\"/Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/\"", "language": "python", "metadata": {}, "outputs": [], "prompt_number": 11 }, { "cell_type": "code", "collapsed": false, "input": "#command for only obtaining the context '__CG_'\n!grep \"[A-Z][A-Z]CG[A-Z]\" <{methratio}methratio_out_M1.txt> {filtered}methratio_out_CG_M1.txt", "language": "python", "metadata": {}, "outputs": [], "prompt_number": 3 }, { "cell_type": "code", "collapsed": false, "input": "#obtaining a filtered file with at least 5x coverage\n!awk '{if ($8 >= 5) print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12}' /Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/methratio_out_CG5x_M1.txt", "language": "python", "metadata": {}, "outputs": [], "prompt_number": 6 }, { "cell_type": "code", "collapsed": false, "input": "!tr ' ' \"\\t\" /Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/methratio_out_CG5x_M1_tab.txt", "language": "python", "metadata": {}, "outputs": [], "prompt_number": 7 }, { "cell_type": "heading", "level": 3, "metadata": {}, "source": "M3" }, { "cell_type": "code", "collapsed": false, "input": "#command for only obtaining the context '__CG_'\n!grep \"[A-Z][A-Z]CG[A-Z]\" <{methratio}methratio_out_M3.txt> {filtered}methratio_out_CG_M3.txt", "language": "python", "metadata": {}, "outputs": [], "prompt_number": 12 }, { "cell_type": "code", "collapsed": false, "input": "#obtaining a filtered file with at least 5x coverage\n!awk '{if ($8 >= 5) print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12}' /Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/methratio_out_CG5x_M3.txt", "language": "python", "metadata": {}, "outputs": [], "prompt_number": 13 }, { "cell_type": "code", "collapsed": false, "input": "!tr ' ' \"\\t\" /Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/methratio_out_CG5x_M3_tab.txt", "language": "python", "metadata": {}, "outputs": [], "prompt_number": 14 }, { "cell_type": "heading", "level": 3, "metadata": {}, "source": "T1D3" }, { "cell_type": "code", "collapsed": false, "input": "#command for only obtaining the context '__CG_'\n!grep \"[A-Z][A-Z]CG[A-Z]\" <{methratio}methratio_out_T1D3.txt> {filtered}methratio_out_CG_T1D3.txt", "language": "python", "metadata": {}, "outputs": [], "prompt_number": 15 }, { "cell_type": "code", "collapsed": false, "input": "#obtaining a filtered file with at least 5x coverage\n!awk '{if ($8 >= 5) print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12}' /Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/methratio_out_CG5x_T1D3.txt", "language": "python", "metadata": {}, "outputs": [], "prompt_number": 16 }, { "cell_type": "code", "collapsed": false, "input": "!tr ' ' \"\\t\" /Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/methratio_out_CG5x_T1D3_tab.txt", "language": "python", "metadata": {}, "outputs": [], "prompt_number": 17 }, { "cell_type": "heading", "level": 3, "metadata": {}, "source": "T1D5" }, { "cell_type": "code", "collapsed": false, "input": "#command for only obtaining the context '__CG_'\n!grep \"[A-Z][A-Z]CG[A-Z]\" <{methratio}methratio_out_T1D5.txt> {filtered}methratio_out_CG_T1D5.txt", "language": "python", "metadata": {}, "outputs": [], "prompt_number": 18 }, { "cell_type": "code", "collapsed": false, "input": "#obtaining a filtered file with at least 5x coverage\n!awk '{if ($8 >= 5) print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12}' /Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/methratio_out_CG5x_T1D5.txt", "language": "python", "metadata": {}, "outputs": [], "prompt_number": 19 }, { "cell_type": "code", "collapsed": false, "input": "!tr ' ' \"\\t\" /Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/methratio_out_CG5x_T1D5_tab.txt", "language": "python", "metadata": {}, "outputs": [], "prompt_number": 20 }, { "cell_type": "heading", "level": 3, "metadata": {}, "source": "T3D3" }, { "cell_type": "code", "collapsed": false, "input": "#command for only obtaining the context '__CG_'\n!grep \"[A-Z][A-Z]CG[A-Z]\" <{methratio}methratio_out_T3D3.txt> {filtered}methratio_out_CG_T3D3.txt", "language": "python", "metadata": {}, "outputs": [], "prompt_number": 21 }, { "cell_type": "code", "collapsed": false, "input": "#obtaining a filtered file with at least 5x coverage\n!awk '{if ($8 >= 5) print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12}' /Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/methratio_out_CG5x_T3D3.txt", "language": "python", "metadata": {}, "outputs": [], "prompt_number": 22 }, { "cell_type": "code", "collapsed": false, "input": "!tr ' ' \"\\t\" /Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/methratio_out_CG5x_T3D3_tab.txt", "language": "python", "metadata": {}, "outputs": [], "prompt_number": 23 }, { "cell_type": "heading", "level": 3, "metadata": {}, "source": "T3D5" }, { "cell_type": "code", "collapsed": false, "input": "#command for only obtaining the context '__CG_'\n!grep \"[A-Z][A-Z]CG[A-Z]\" <{methratio}methratio_out_T3D5.txt> {filtered}methratio_out_CG_T3D5.txt", "language": "python", "metadata": {}, "outputs": [], "prompt_number": 24 }, { "cell_type": "code", "collapsed": false, "input": "#obtaining a filtered file with at least 5x coverage\n!awk '{if ($8 >= 5) print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12}' /Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/methratio_out_CG5x_T3D5.txt", "language": "python", "metadata": {}, "outputs": [], "prompt_number": 25 }, { "cell_type": "code", "collapsed": false, "input": "!tr ' ' \"\\t\" /Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/methratio_out_CG5x_T3D5_tab.txt", "language": "python", "metadata": {}, "outputs": [], "prompt_number": 26 }, { "cell_type": "code", "collapsed": false, "input": "#NOTEBOOK NAME\nnb='Filtering_Larvae_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": 1 }, { "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": 2 }, { "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/Filtering_Larvae_AdapterTrimmed.ipynb to html\r\n[NbConvertApp] Support files will be in Filtering_Larvae_AdapterTrimmed[0408_1223]_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 209885 bytes to Filtering_Larvae_AdapterTrimmed[0408_1223].html\r\n" } ], "prompt_number": 3 }, { "cell_type": "code", "collapsed": false, "input": "", "language": "python", "metadata": {}, "outputs": [] } ], "metadata": {} } ] }