{
 "metadata": {
  "name": "Concatenate_Larvae_Files"
 },
 "nbformat": 3,
 "nbformat_minor": 0,
 "worksheets": [
  {
   "cells": [
    {
     "cell_type": "heading",
     "level": 3,
     "metadata": {},
     "source": "I'm going to concatonate the Sept and Nov runs from my Larvae data (R1 and R2 separately)"
    },
    {
     "cell_type": "heading",
     "level": 3,
     "metadata": {},
     "source": "F_R1"
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "!cat /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Nov/filtered_BS_CgF_TTAGGC_L004_R1.fastq /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Sept/filtered_BS_CgF_TTAGGC_L007_R1.fastq > /Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/F_R1.fastq",
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 1
    },
    {
     "cell_type": "heading",
     "level": 3,
     "metadata": {},
     "source": "M1_R1"
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "!cat /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Nov/filtered_BS_CgM1_ACTTGA_L004_R1.fastq /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Sept/filtered_BS_CgM1_ACTTGA_L007_R1.fastq > /Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/M1_R1.fastq",
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 2
    },
    {
     "cell_type": "heading",
     "level": 3,
     "metadata": {},
     "source": "M3_R1"
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "!cat /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Nov/filtered_BS_CgM3_GATCAG_L004_R1.fastq /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Sept/filtered_BS_CgM3_GATCAG_L007_R1.fastq > /Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/M3_R1.fastq",
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 3
    },
    {
     "cell_type": "heading",
     "level": 3,
     "metadata": {},
     "source": "T1D3_R1"
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "!cat /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Nov/filtered_BS_CgLarv_T1D3_TGACCA_L004_R1.fastq /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Sept/filtered_BS_CgLarv_T1D3_TGACCA_L007_R1.fastq > /Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T1D3_R1.fastq",
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 4
    },
    {
     "cell_type": "heading",
     "level": 3,
     "metadata": {},
     "source": "T1D5_R1"
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "!cat /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Nov/filtered_BS_CgLarv_T1D5_ACAGTG_L004_R1.fastq /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Sept/filtered_BS_CgLarv_T1D5_ACAGTG_L007_R1.fastq >  /Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T1D5_R1.fastq",
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 5
    },
    {
     "cell_type": "heading",
     "level": 3,
     "metadata": {},
     "source": "T3D3_R1"
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "!cat /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Nov/filtered_Bs_CgLarve_T3D3_GCCAAT_L004_R1.fastq /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Sept/filtered_Bs_CgLarve_T3D3_GCCAAT_L007_R1.fastq > /Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T3D3_R1.fastq",
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 6
    },
    {
     "cell_type": "heading",
     "level": 3,
     "metadata": {},
     "source": "T3D5_R1"
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "!cat /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Nov/filtered_BS_CgLarv_T3D5_CAGATC_L004_R1.fastq /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Sept/filtered_BS_CgLarv_T3D5_CAGATC_L007_R1.fastq > /Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T3D5_R1.fastq ",
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 7
    },
    {
     "cell_type": "heading",
     "level": 3,
     "metadata": {},
     "source": "F_R2"
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "!cat /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Nov/filtered_BS_CgF_TTAGGC_L004_R2.fastq /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Sept/filtered_BS_CgF_TTAGGC_L007_R2.fastq > /Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/F_R2.fastq",
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 8
    },
    {
     "cell_type": "heading",
     "level": 3,
     "metadata": {},
     "source": "M1_R2"
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "!cat /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Nov/filtered_BS_CgM1_ACTTGA_L004_R2.fastq /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Sept/filtered_BS_CgM1_ACTTGA_L007_R2.fastq > /Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/M1_R2.fastq ",
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 9
    },
    {
     "cell_type": "heading",
     "level": 3,
     "metadata": {},
     "source": "M3_R2"
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "!cat /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Nov/filtered_BS_CgM3_GATCAG_L004_R2.fastq /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Sept/filtered_BS_CgM3_GATCAG_L007_R2.fastq >  /Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/M3_R2.fastq ",
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 10
    },
    {
     "cell_type": "heading",
     "level": 3,
     "metadata": {},
     "source": "T1D3_R2"
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "!cat /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Nov/filtered_BS_CgLarv_T1D3_TGACCA_L004_R2.fastq /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Sept/filtered_BS_CgLarv_T1D3_TGACCA_L007_R2.fastq >  /Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T1D3_R2.fastq ",
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 11
    },
    {
     "cell_type": "heading",
     "level": 3,
     "metadata": {},
     "source": "T1D5_R2"
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "!cat /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Nov/filtered_BS_CgLarv_T1D5_ACAGTG_L004_R2.fastq /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Sept/filtered_BS_CgLarv_T1D5_ACAGTG_L007_R2.fastq > /Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T1D5_R2.fastq  ",
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 12
    },
    {
     "cell_type": "heading",
     "level": 3,
     "metadata": {},
     "source": "T3D3_R2"
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "!cat /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Nov/filtered_Bs_CgLarve_T3D3_GCCAAT_L004_R2.fastq /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Sept/filtered_Bs_CgLarve_T3D3_GCCAAT_L007_R2.fastq > /Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T3D3_R2.fastq  ",
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 13
    },
    {
     "cell_type": "heading",
     "level": 3,
     "metadata": {},
     "source": "T3D5_R2"
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "!cat /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Nov/filtered_BS_CgLarv_T3D5_CAGATC_L004_R2.fastq /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Sept/filtered_BS_CgLarv_T3D5_CAGATC_L007_R2.fastq > /Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T3D5_R2.fastq   ",
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 14
    },
    {
     "cell_type": "heading",
     "level": 4,
     "metadata": {},
     "source": "Script to take html snapshot of IPython notebook"
    },
    {
     "cell_type": "raw",
     "metadata": {},
     "source": "Notes from Steven's notebook: http://nbviewer.ipython.org/urls/dl.dropboxusercontent.com/u/115356/ip/nbview/_IPsnapshot.ipynb"
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "#NOTEBOOK NAME\nnb='Concatenate_Larvae_Files'\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": 12
    },
    {
     "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": 13
    },
    {
     "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/Concatenate_Larvae_Files.ipynb to html\r\n[NbConvertApp] Support files will be in Concatenate_Larvae_Files[0331_1102]_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 208617 bytes to Concatenate_Larvae_Files[0331_1102].html\r\n"
      }
     ],
     "prompt_number": 14
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "",
     "language": "python",
     "metadata": {},
     "outputs": []
    }
   ],
   "metadata": {}
  }
 ]
}