puzzle club 3: Calculating GC content

GC_Julia.ipynb

GC_python.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Computing GC content\n",
    "---------------------\n",
    "\n",
    "Return the string with the highest GC content and the percentage GC content"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Rosalind_0409 \n",
      "52.4144869215\n"
     ]
    }
   ],
   "source": [
    "from __future__ import division\n",
    "from Bio import SeqIO\n",
    "\n",
    "file = '/home/scott/Downloads/rosalind_gc.txt'\n",
    "fasta_file = SeqIO.parse(open(file), 'fasta')\n",
    "with open(file):\n",
    "\tmax_value = None\n",
    "\tfor fasta in fasta_file:\n",
    "\t\tname, s = fasta.id, str(fasta.seq)\n",
    "\t\tcontent  = ((s.count('G') + s.count('C')) / len(s)) * 100\n",
    "\t\tif content > max_value: max_name, max_value = name, content   \n",
    "            \n",
    "print max_name, '\\n', max_value"
   ]
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "Python 2",
   "language": "python",
   "name": "python2"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 2
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython2",
   "version": "2.7.6"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 0
}

GC_R.ipynb