{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "This notebook includes efforts in trying to better understand the relationship of contigs that have similar annotations. "
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "<img src=\"http://eagle.fish.washington.edu/cnidarian/skitch/Downloads___EchinoBase_1AFC08C4.png\" alt=\"Downloads___EchinoBase_1AFC08C4.png\"/>"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      ">PMI_010847-RA\r\n",
      "ANIEIFLPRIEAVVLFGEPVRWETNLQLILDMLITNGQLNHTPDHVPYPNMPVLGCNVDLMWMSEAHLPRLGHGSFMVCLESLYKKITGRDLLYTVLTGKPSQITYHCAENVLSQQARAMGCQGPLRTLYAIGDNPMTDIYGANLYNQYLTAKAAKGLQKPGSRQPAAIRQGVVMSDPHDDIHIETSAQVDVSDHPVHEIDDHVCESEALMTDNFDDGYPVTMESVLVYTGLHSKPGEVGQMDEAHLELDHGHRDFEFNKALIQPTITAQHVRDAVDIIFDREGFK\r\n",
      ">PMI_010846-RA\r\n",
      "MAAAARSLQRILPRNCSHLKNCISVFNHPKRFFSIRTELHSKHPPFGILFDIDGVIVRGKRILHEAVEAFQKLSDGEGHLRVPVVFVTNAGNKLRQNKAKQLTEWLGIKIHPDQVVMSHSPLKMFPQFHDKHVLVSGQGPIKEIAKGLGFTRVTTVEEVRDMFPHLDMVDHQRRVPAPNV\r\n",
      ">PMI_010849-RA\r\n",
      "MFQTRSEYDRGVNTFSPEGRLFQVEYAIEAIKLGSTALGIQTSEGCVLAVEKRITSPLMEISSIEKIVEVDNHIGCAMSGLIADSRTLIDRARVEAQSHWFTYNEKMSIEAVTQAVSNLAMQFGDDDADSGAMIPHGSIRHIHSSMTLKEACKEALVILKQVMEEKLSSTNVEMATVTREKKFVMFTKEEIEAIVAEM\r\n",
      ">PMI_010848-RA\r\n",
      "MSYPYHMESDDSFDYLFKIVLIGDAGVGKTCVVQRFKSGTFLEKQHSTIGVDFTMKSLTVDGKKVKLQVWDTAGQERFRTITQSYYRSANGVIIAYDITKKETFNNVPRWIEDVHKYAGNSVAQVLIGNKKDLDELRQVDFEDAQAIAQHHGMLQCLETSAKDSTNVEQTFALLAQELKRRHAGGAALDGGDSLKLNYNAKRVDGWNCCG\r\n",
      ">PMI_010850-RA\r\n",
      "MQTSGGQDHLCINPEIYCKKIQGTSVRSTSSDLPQRKYQRQLSIAMATSLGARKPTSIQRPKRWSEEVEEAYRLQLAGYRDALEYHSVKGESGYIKKLQRKDGNYYYYNRSRECADKDVNKIKLYGY\r\n"
     ]
    }
   ],
   "source": [
    "!head ./misc/Pm_proteins.fasta"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "29805\r\n"
     ]
    }
   ],
   "source": [
    "!fgrep -c \">\" ./misc/Pm_proteins.fasta"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Creating blast database"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "!makeblastdb \\\n",
    "-in ./misc/Pm_proteins.fasta \\\n",
    "-dbtype prot \\\n",
    "-out ./misc/Pm_proteins"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "**Blasting**"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "!blastx \\\n",
    "-query ./data/Phel_transcriptome.fasta \\\n",
    "-db ./data/Pm_proteins \\\n",
    "-out ./wd/Phel_blastx_Pm_e50.tab \\\n",
    "-evalue 1E-50 \\\n",
    "-max_target_seqs 1 \\\n",
    "-max_hsps 1 \\\n",
    "-outfmt 6 \\\n",
    "-num_threads 6"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Identifying the # of Phel contigs that match to the same PMI protein:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "   4 PMI_020736-RA\r\n",
      "   4 PMI_023204-RA\r\n",
      "   4 PMI_025724-RA\r\n",
      "   4 PMI_028024-RA\r\n",
      "   5 PMI_000929-RA\r\n",
      "   5 PMI_001602-RA\r\n",
      "   5 PMI_003081-RA\r\n",
      "   5 PMI_017390-RA\r\n",
      "   5 PMI_019456-RA\r\n",
      "   6 PMI_000110-RA\r\n",
      "   6 PMI_013600-RA\r\n",
      "   7 PMI_010001-RA\r\n",
      "   7 PMI_020859-RA\r\n",
      "   8 PMI_015266-RA\r\n",
      "  10 PMI_029345-RA\r\n"
     ]
    }
   ],
   "source": [
    "!cut -f2 ./wd/Phel_blastx_Pm_e50.tab | sort | uniq -c | sort \\\n",
    "> ./wd/Duphits_Phel_blastx_Pm_e50.tab\n",
    "!tail -15 ./wd/Duphits_Phel_blastx_Pm_e50.tab \n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Identifying specific Phel contigs and where the match knowing that columns are `qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore`"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Phel_contig_16086\tPMI_000929-RA\t35.38\t359\t205\t9\t16\t1056\t41\t384\t2e-59\t  211\r\n",
      "Phel_contig_2292\tPMI_000929-RA\t38.33\t600\t323\t13\t5150\t3441\t1175\t1757\t1e-108\t  383\r\n",
      "Phel_contig_6114\tPMI_000929-RA\t59.97\t657\t214\t4\t2252\t354\t1125\t1756\t0.0\t  813\r\n",
      "Phel_contig_619\tPMI_000929-RA\t45.31\t651\t313\t8\t5890\t4061\t1109\t1757\t2e-169\t  570\r\n",
      "Phel_contig_6408\tPMI_000929-RA\t45.16\t558\t271\t10\t1586\t3\t1136\t1688\t9e-151\t  481\r\n"
     ]
    }
   ],
   "source": [
    "!fgrep \"PMI_000929-RA\" ./wd/Phel_blastx_Pm_e50.tab"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "collapsed": true
   },
   "source": [
    "This 'fgrep' can be done repeatedly and overlaps determined manually."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  }
 ],
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