{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "## Install biopython\n",
    "\n",
    "in the terminal run the following command:\n",
    "\n",
    "conda install -c https://conda.anaconda.org/anaconda biopython"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "# importing some features of Biopython\n",
    "from Bio import SeqIO"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      ">Geo_Pool_F_GGCTAC_L006_R1_001_val_1_(paired)_contig_1\r\n",
      "TGAGTTTGAATCCCCGCCTGGCCAGTCTCCGTGATTATTGACATACAACATTGCCTTTTG\r\n",
      "TTGTCATTAGTCTCTCAACACTGATTCAAATGGGAAAGTTATCAATTACTTGTAGGGATG\r\n",
      "TGTGCTGGAGTACTTGTTAACCATTCAGGGTCCCAGGAAGTAGTGGTTAAGTTAACTGCA\r\n",
      "ATCTCATTAAAATTATATCGACTTTAGGCTTCCATACACTACGCACAGTAGATCTGATGG\r\n",
      "TGTTGCATAGAACGTCACATCAGATTGCCCTTTCTGCCAGCCCATGTTTAATGTAAATGA\r\n",
      "TTTTCAGAAATTACAGAAGTCAGGGATGATACAGGGACTTTTTTTATTTATACATTAATG\r\n",
      "ACACAAGATCAGTCTGAGGTGACCTTTAATGCAATGCTGCCAGCTCTACTGTGTGTAGGG\r\n",
      "TATGGAAGTTGATCTGATTTTAATAAGATCGTCTGTAAGTCTTCGATGACATAAAAGTGA\r\n",
      "TGCTAAATATTCAAACAANNAAAAATAATCGGGCAAAATAATATTTGTTTACTTACTTGT\r\n"
     ]
    }
   ],
   "source": [
    "# seeing a fasta file\n",
    "!head \"/Users/migueldelrio/mdelrio2-btae-nb/data/Geo_Female.fa\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "datafile=\"/Users/migueldelrio/mdelrio2-btae-nb/data/Geo_Female.fa\""
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# you have to know which contig you are looking for "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "# defining the contig to search\n",
    "search_contig= \"Geo_Pool_F_GGCTAC_L006_R1_001_val_1_(paired)_contig_105\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "> Geo_Pool_F_GGCTAC_L006_R1_001_val_1_(paired)_contig_105\t1999\n",
      "AGTTAAATTAAAGTCTTCACAGAGAACTGCGGGAATAACTTGAAAGAAGGTGACGTCGGGTAGTGGAGGAAATCCATGACAGTTTAGGACGTTTTTCGAACGGTTGGAACAGTAGTGAACATCAGCAAGTAGACGCTTGCACAGATGCATGTCCTGCAACGTGCAGATACGAGCCCGGGACAGAAACCGGATGCACTGTGTAAAGTGTGCGGCGACAAAGCGTCCGGTAAACACTACGGCGTTCAGAGCTGTGACGGATGCAGGGGATTTTTCAAGCGTAGCATCCGCCGAAGTTTAGAGTATGTATGTAAGGAGAACGGGAGCTGTATTGTGGACGTGGCCCGCCGGAACCAGTGTCAGGCATGCAGGTTCAAGAAATGTCTAGATGTCAATATGAATAAAGACGCGGTCCAACATGAACGCGCGCCTCGGTGCTACCAGTATCGGAGAGAAAGCCAAGATTTCCCCAGGGCAAGTGAAGAGCGGCATTCTCCCTACCCCACGGGGGAATACTTGGACAGAGCCAGGTCAGAATTTCGCCACTTTCCGTCATATTCATCACCAGCAGGGTTCACACCGGAGTACGGATTCAACGCTGGCTTCCACTCCAATGCATTCCACATGAACGACATCCGACGAGCGAGTCAACATCAGTACCCCAGTCACATTACACACAACATCAGCCCTCTGTCAGAAACCGGCAGCTCCAGTCATTTCCACTTAAACCGATATCCAAATGACGCACCTCCGCATTTTGGAAATTTTAACGGAAGGCTGGACCGAAGTTTTGGACTGACGAACGCATTTGCGCCTGGAAGACGACCTCACATTAATCATTTCCCTGCACCACCAGCAAGCATTTCCGGCAACTTCATGAACAACATCACACAAGGCAGGCCGTTGTTATTAGAGCCCAGACACGAACCAAGTAGAAACGGAAGTCATTCGAATCATTCTACGGAGATTGATGACATGAAGACGGAGAAAGCCGACTCCGAAGATGAACTCCCCGATAAGGTTTCTGTGTCCAGATCTCCCTCACCATCAACATCGGAAGGGGCAAGCCCTAAGTCTGTAGGAGACAGCGGTATCATGGCGGACCGAAGTCCCTCCCCTGCAGCGTCTAAGTCATCCACAGAATGTAATGATGTCAAAGATTCTCCGGACAACACTTCAAGCGGCAGTCCTATTGTTTCATCAACCGTGACGTCGTCTGCTCCAGATCACGTGCCGCCCTTTGTTCCTAAATACATGCCCAGCAATAGTCTATTCAACATCGCATCACTGTATCCCAACTACAACAACCGAAACGAAAGCCAGATGATGTCTAACTCTCCACACACGCCGTTGGATTCAACATACGAAACTGCGGCTAAATTGCTGTTTATGTCCATAAAATGGGCGCGCAATATCCCATCATTCCTCTCACTTCCGTTCCGGGATCAGGCCATTCTATTGGAGGAGTCCTGGAGTGAACATTTCATATTAAGTGCTGCGCAATGGTCACTTCCGCTAGATATAAGTGCTTTAATGGCGTCAAATGGGTACTCCGCAACCGACCAATCAGATCGTGCCATGATAATCAACGCCCAGCTGAAGACTTTACAGGAAGTGATGTCACGCTTCGCCGCAATGAGAGTGGATTCTACAGAGTACGCATGTCTGAAGGCTCTTGTTCTGTTTAAGTCGGAGATAAAAGGTCTGCGAGATTATCTCCATGTTGAGATGCTGCAGGATCAAGCCCAGGTGATGTTGGGCGACTACACGTACACAAACCACCCAACCAGCAAGACCCGCTTCGGCAAGCTCCTCCTCCTCCTCCCCATCCTCAGGACCATTAGCCCCCGCTCCATCGAGGAGGTGTTCTTCCGGCGCACCATTGGCAGCATACCTATTGAGCGACTCCTCTGTGACATGTTCAAATCTAGTTAACAAGTCAGATACATTTGTATGTTATGTATGGTGGGTTAGCAGAGCCAACACGAACTTATAACTGACC\n"
     ]
    }
   ],
   "source": [
    "for seq_record in SeqIO.parse(datafile, \"fasta\"):\n",
    "    if seq_record.id== search_contig:\n",
    "        print(\"> \"+seq_record.id+ \"\\t\"+str(len(seq_record)))\n",
    "        print(seq_record.seq)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  }
 ],
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  "kernelspec": {
   "display_name": "Python 3",
   "language": "python",
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  "language_info": {
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   "file_extension": ".py",
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   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
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