{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Determining how complete the transcriptome is..."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "  307964 ../data-results/Geoduck-transcriptome-v3.fa\r\n"
     ]
    }
   ],
   "source": [
    "#fasta with non-euk removed\n",
    "!wc -l ../data-results/Geoduck-transcriptome-v3.fa"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Compare with C. gigas"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current\n",
      "                                 Dload  Upload   Total   Spent    Left  Speed\n",
      "100 11.6M  100 11.6M    0     0  1317k      0  0:00:09  0:00:09 --:--:-- 2284k\n"
     ]
    }
   ],
   "source": [
    "!curl ftp://ftp.ensemblgenomes.org/pub/metazoa/release-29/fasta/crassostrea_gigas/cdna/Crassostrea_gigas.GCA_000297895.1.29.cdna.all.fa.gz \\\n",
    "> analyses/Crassostrea_gigas.GCA_000297895.1.29.cdna.all.fa.gz"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "!gunzip analyses/Crassostrea_gigas.GCA_000297895.1.29.cdna.all.fa.gz"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "27108\r\n"
     ]
    }
   ],
   "source": [
    "!fgrep -c \">\" analyses/Crassostrea_gigas.GCA_000297895.1.29.cdna.all.fa"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "\n",
      "Building a new DB, current time: 11/17/2015 12:48:34\n",
      "New DB name:   analyses/Crassostrea_gigas.GCA_000297895.1.29.cdna\n",
      "New DB title:  analyses/Crassostrea_gigas.GCA_000297895.1.29.cdna.all.fa\n",
      "Sequence type: Nucleotide\n",
      "Keep Linkouts: T\n",
      "Keep MBits: T\n",
      "Maximum file size: 1000000000B\n",
      "Adding sequences from FASTA; added 27108 sequences in 2.71984 seconds.\n"
     ]
    }
   ],
   "source": [
    "!makeblastdb \\\n",
    "-dbtype nucl \\\n",
    "-in analyses/Crassostrea_gigas.GCA_000297895.1.29.cdna.all.fa \\\n",
    "-out analyses/Crassostrea_gigas.GCA_000297895.1.29.cdna"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "!blastn \\\n",
    "-task blastn \\\n",
    "-query ../data-results/Geoduck-transcriptome-v3.fa \\\n",
    "-db analyses/Crassostrea_gigas.GCA_000297895.1.29.cdna \\\n",
    "-num_threads 4 \\\n",
    "-evalue 1e-30 \\\n",
    "-max_target_seqs 1 \\\n",
    "-max_hsps 1 \\\n",
    "-outfmt 6 \\\n",
    "-out analyses/Geoduck-v3_blastn_Cgigas_cdna.out"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 28,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "    8395 analyses/Geoduck-v3_blastn_Cgigas_cdna_e10.out\r\n"
     ]
    }
   ],
   "source": [
    "!blastn \\\n",
    "-task blastn \\\n",
    "-query ../data-results/Geoduck-transcriptome-v3.fa \\\n",
    "-db analyses/Crassostrea_gigas.GCA_000297895.1.29.cdna \\\n",
    "-num_threads 8 \\\n",
    "-evalue 1e-10 \\\n",
    "-max_target_seqs 1 \\\n",
    "-max_hsps 1 \\\n",
    "-outfmt 6 \\\n",
    "-out analyses/Geoduck-v3_blastn_Cgigas_cdna_e10.out \n",
    "!wc -l analyses/Geoduck-v3_blastn_Cgigas_cdna_e10.out"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 27,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "## Compare with Ruphibase"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "32606\r\n"
     ]
    }
   ],
   "source": [
    "!grep -c \"rud\" /Users/sr320/Desktop/query.txt"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "ruditapes2_lrc7040\tATTCAAATCTCTAACACTGATTCATACATGTAATAACTTGGCATACTATACATTATCAACATGTACTGTTACTTTCCTGTAATTGTTCAAAATATCTCTGGAATATTTTACACTTTATCTGTGGTTTTTTACAGTTTTTTTTTAATTGAAATAGTGATAACTTTGATTGAACATTCTTTTATGTTTTAGCATCAAGATCTTCAAACTTGTAATACACACAATATCAATAACAAAATGTGACAGTTTTATTTTCATTCATCATACACATCTTCCTTATCACATACATACTGACATAGATTCTGGTGTCATAAGACGGTCTGCATCTTGGTCAGGTATTTCAAATCTAAATTCATCTTCCATTGCCATGATAACTTCTACAACATCTAAACTGTCCAATCCTAAATCATTCATAAAGTGTGAAGTCAATGACAGCTTTTCGGGATCAACTTTATCATAAAGTTGCAAAACGAGAATGACTCTTTCTTTAACATGAGATATTGTGAGAGCTGGCTTCTGACCATAATATCGAGGGTTTTGAATTGCAGTTTTCTGTGGTGCTAATAATTTTGTTGAATTTCTGCAATTGTGAATCGTTCTGTCTTCTTGTCTGCAATGGAGTAGTGAGACAGAAGATACACGTGGAAAGACGNTTCTAGCAACAGTTTGGAGGCAATTTGTTGCCCGGACCGTCTTCAGCAAGGTGG\r",
      "\r\n"
     ]
    }
   ],
   "source": [
    "#Results from webform download\n",
    "!head -1 /Users/sr320/Desktop/query.txt"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "!awk '{print \">\"$1\"\\n\"$2}' /Users/sr320/Desktop/query.txt \\\n",
    "> analyses/RuphiBase_32606.fa"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {
    "collapsed": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      ">ruditapes2_lrc7040\r\n",
      "ATTCAAATCTCTAACACTGATTCATACATGTAATAACTTGGCATACTATACATTATCAACATGTACTGTTACTTTCCTGTAATTGTTCAAAATATCTCTGGAATATTTTACACTTTATCTGTGGTTTTTTACAGTTTTTTTTTAATTGAAATAGTGATAACTTTGATTGAACATTCTTTTATGTTTTAGCATCAAGATCTTCAAACTTGTAATACACACAATATCAATAACAAAATGTGACAGTTTTATTTTCATTCATCATACACATCTTCCTTATCACATACATACTGACATAGATTCTGGTGTCATAAGACGGTCTGCATCTTGGTCAGGTATTTCAAATCTAAATTCATCTTCCATTGCCATGATAACTTCTACAACATCTAAACTGTCCAATCCTAAATCATTCATAAAGTGTGAAGTCAATGACAGCTTTTCGGGATCAACTTTATCATAAAGTTGCAAAACGAGAATGACTCTTTCTTTAACATGAGATATTGTGAGAGCTGGCTTCTGACCATAATATCGAGGGTTTTGAATTGCAGTTTTCTGTGGTGCTAATAATTTTGTTGAATTTCTGCAATTGTGAATCGTTCTGTCTTCTTGTCTGCAATGGAGTAGTGAGACAGAAGATACACGTGGAAAGACGNTTCTAGCAACAGTTTGGAGGCAATTTGTTGCCCGGACCGTCTTCAGCAAGGTGG\r",
      "\r\n",
      ">ruditapes2_c3688\r\n",
      "ATGTATTGTCGCATAAGAATAAATTTTCGGATAGTTAACAAGTGGAATATAGCAGACGTATTTGAACCGTGGGCTTGTTTCAAGTATCATGGCGAATGACTTCCTTATCTCAAAGTGGAAGCGATGGTTCAGTTTATTTGATGGCAATAATGATGGCAAAGTTTGCTTTGCAGACATGGAGAAAGCCAGAGATAAATTTACAAAGCAACATGAGTTGAAAGATGACGAAAAGAAGGAAATAAGTGAGAAATTCACGAAATGGTGGTGCGAATATGTGAACTGGGGAAAAGAAGAATTGACGGTGGACGAGTTTGCAGAATACCAAAATGCTGCATTTAAAGCCGACAAAGAAAAGTTTGTTGAGCGAATTAAAAAGTGTCAAGCTGAGATTGGTGACTTTGTAGACGTCGCGCACGATGGTTTGTTTCCGAAAGGAAGCTTTGGCAATCCTCAAGGCGGAGGGGCACGAGGACGAAGAGAA\r",
      "\r\n",
      ">ruditapes2_c1400\r\n",
      "GTCACTAGTGACGGAAATGGTTATGGGTATGTTGCCAGCGGAACAAGCTCGCCCTCTCCGAGTCTCTCAAGCCCACAGTACCCGGTCAACATTTCGTACTATGCAGACCCAAACTATATGAAAGAGGTGTCAGCAAGTCCATTACATGTGGCTGTAGGGGCACAAGTATACGTCAAGGTCTTTACAGAGACATACGACTGGAACGCTAGAATGAGAGTCGTTTCCTGTTACACTAAACCAACCTACAATGCGCCTGATCATACAAAATATTACCTTCTCGAGAACGGGTGTGAAGTTGACACGAACACGCATATTATTTCACAATCCTCCCACGAGACTAAATTTGTCTTCGACAATTTTGAGTACACAAGCAACCACGAGGGCATCTACATGTTTTGCGACACCATCTTTTGCAACACGCATGATTACTCGGCAAAATGTAGGCAGTCTTGCAACCCGGTAATTCGGAGGAAAATTTCTGTGGAAAATGTACCGTCTGATGATAAGGAAGCTGATAAGTCATCGGATGTTACTAATCAGGATTCTTAAAGAAAGCAGACGACTCTAGATGACCAAAAATGATTGAAATAGAAACATAATTGTTTTCTTTATTTGATTTATCAACTGGAAAATTTTGATTTTCTTGAGACTACTTGACAGTTACAATGAAAATTTATGGCATTTATCAGATTTAGTTCTTCTTCTGCACAGAATTTTTAGTATGGTTTATTAAAATTACACTTGTAT\r",
      "\r\n",
      ">ruditapes2_c3682\r\n",
      "CTTTATTTACACATTACATTTAAACTTTTAAAAATGAAATCAGTTAAACCAGATAAAGTACATATATACTAAAGTCACTCCACTGTTCTCTATAAACAATAAGTATCATTCATTACACATTTGCACAAGGAAGATAAAATCTTAATTGCTTCAGTAATTAAACAATTAGTCTCCAACCTATTACTACTACACAACTTTTGATGACACAATATTTTTCATCACAGAATTGTTTCCATTTCTCATTTAGCCTCGCCCTCTTGTTTACCTCGGAGATGAAATGGTACATATTCTGGTTTTCCTTTAAGCGCTCGTCTTTTCTTCATTTCATCTTTGAAATCTTCGTGTTCATCTCTAAATAAACCATGATCTCGAAGTCCATCCATAAGTTGTTTTAGCTCTACGTGACGAGGGTAGTAATCTACATTATAATAAGGATCCATATGTGGCGGTTTGCCAGAAAATATTCTTAGAACTTTTGTAGATTTCACATCTGTCTCTCTGGATAGCTCTCCAAATATTTTGGCAGAGAGTTTCGCCATACGCCGTGCATAATTTGATGATGACATCATTCACTGCTTTTGTTCCTTTCAAACATTTGGATGTTGTTAACGACTAAATTTATGATCTAAGATCACTTGGCAGAGGTGCCATTGGGGGGCAATACACAGTTTTCAAGGCTTCTCGGCAAACAACTGACTGCGCCACAATCAAAACCTCACACACAAGTCTGTAATCACACACTTTTTTCACTATTTTAAGTCTTCTGAATACCTTAAATGAAGAGCTCTCTAAAGT\r",
      "\r\n",
      ">ruditapes2_c4432\r\n",
      "CCATTGTGGAGCCGACAGATTCCATACACAATGATGAAGTTTGCCTGCTATAAACTGCTAAGTAGAAGCTCTGTACAAGTATGTTGTACCAAAACCAAGGTCAGAGTGCACAAAAGGAGAGCAGTTGGTTGTTACATTTATGGCTGGTTACATTGCTGGAGTATTCCGTGCTATTGTGTCCCATCCTGCTGATACAATCGTGTCCAAGCTGAACACAGATGCTGGAAGTACTGCCGTGGAAGCTGCAAAGGCTCTTGGATTCAAGGGATTGTGGAAGGGTCTGTTCCCCAGGATTATCATGATTGGTACACTGACCGCCCTGCAGTGGTTTATCTACGACTCTGTGAAGGTGTTCTTCCGTCTACCACGTCCACCACCGCCAGAGATGCCCGCCAGTCTCAAGAAAAAGCTTGGCATCACTGAATAATGACATTCTAACATAGGAAATAATAAATTGACTATACTTTACTTGTGATTTGACAGATTTTTATACAAAACATTGACGCATAAAGTTTACAAAAAGAATAAAAACGTATCAAAATGTTTGAAAAGAGATTTATTTAATGAAGCACTGTTACTGAACAAAGAT\r",
      "\r\n"
     ]
    }
   ],
   "source": [
    "!head analyses/RuphiBase_32606.fa"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "\n",
      "Building a new DB, current time: 11/17/2015 13:00:03\n",
      "New DB name:   analyses/RuphiBase_32606\n",
      "New DB title:  analyses/RuphiBase_32606.fa\n",
      "Sequence type: Nucleotide\n",
      "Keep Linkouts: T\n",
      "Keep MBits: T\n",
      "Maximum file size: 1000000000B\n",
      "Adding sequences from FASTA; added 32606 sequences in 0.991654 seconds.\n"
     ]
    }
   ],
   "source": [
    "!makeblastdb \\\n",
    "-dbtype nucl \\\n",
    "-in analyses/RuphiBase_32606.fa \\\n",
    "-out analyses/RuphiBase_32606"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "!blastn \\\n",
    "-task blastn \\\n",
    "-query ../data-results/Geoduck-transcriptome-v3.fa \\\n",
    "-db analyses/RuphiBase_32606 \\\n",
    "-num_threads 4 \\\n",
    "-evalue 1e-30 \\\n",
    "-max_target_seqs 1 \\\n",
    "-max_hsps 1 \\\n",
    "-outfmt 6 \\\n",
    "-out analyses/Geoduck-v3_blastn_RuphiBase.out"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "    1410 analyses/Geoduck-v3_blastn_RuphiBase.out\r\n"
     ]
    }
   ],
   "source": [
    "!wc -l analyses/Geoduck-v3_blastn_RuphiBase.out"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "!blastn \\\n",
    "-task blastn \\\n",
    "-query ../data-results/Geoduck-transcriptome-v3.fa \\\n",
    "-db analyses/RuphiBase_32606 \\\n",
    "-num_threads 4 \\\n",
    "-evalue 1e-60 \\\n",
    "-max_target_seqs 1 \\\n",
    "-max_hsps 1 \\\n",
    "-outfmt 6 \\\n",
    "-out analyses/Geoduck-v3_blastn_RuphiBase_e60.out"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 26,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "    2859 analyses/Geoduck-v3_blastn_RuphiBase_e10.out\r\n"
     ]
    }
   ],
   "source": [
    "!blastn \\\n",
    "-task blastn \\\n",
    "-query ../data-results/Geoduck-transcriptome-v3.fa \\\n",
    "-db analyses/RuphiBase_32606 \\\n",
    "-num_threads 8 \\\n",
    "-evalue 1e-10 \\\n",
    "-max_target_seqs 1 \\\n",
    "-max_hsps 1 \\\n",
    "-outfmt 6 \\\n",
    "-out analyses/Geoduck-v3_blastn_RuphiBase_e10.out\n",
    "!wc -l analyses/Geoduck-v3_blastn_RuphiBase_e10.out"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  }
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