spark - let file name as key

spark-let-filename-as-key.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Initial Spark Config"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Welcome to\n",
      "      ____              __\n",
      "     / __/__  ___ _____/ /__\n",
      "    _\\ \\/ _ \\/ _ `/ __/  '_/\n",
      "   /__ / .__/\\_,_/_/ /_/\\_\\   version 1.4.0\n",
      "      /_/\n",
      "\n",
      "Using Python version 2.7.6 (default, Sep  9 2014 15:04:36)\n",
      "SparkContext available as sc, HiveContext available as sqlContext.\n"
     ]
    }
   ],
   "source": [
    "import os\n",
    "import sys\n",
    "\n",
    "spark_home = os.environ.get('SPARK_HOME', None)\n",
    "sys.path.insert(0, spark_home + \"/python\")\n",
    "\n",
    "# Add the py4j to the path.\n",
    "# You may need to change the version number to match your install\n",
    "sys.path.insert(0, os.path.join(spark_home, 'python/lib/py4j-0.8.2.1-src.zip'))\n",
    "\n",
    "# Initialize PySpark to predefine the SparkContext variable 'sc'\n",
    "execfile(os.path.join(spark_home, 'python/pyspark/shell.py'))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Parse Every File"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "from pyspark.sql import SQLContext, Row\n",
    "sqlContext = SQLContext(sc)\n",
    "\n",
    "# get file list in a folder\n",
    "import glob\n",
    "flist =glob.glob(\"./sequence/*\")\n",
    "\n",
    "# parse every file\n",
    "rf = []\n",
    "for f in flist :\n",
    "    lines = sc.textFile(f)\n",
    "    parts = lines.map(lambda l: l.split(\"|\"))\n",
    "    rf.append(parts.map(lambda x : [f] + x))\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Union all file to one rdd"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['./sequence/Sida yellow vein virus.fasta',\n",
       " u'>gi',\n",
       " u'167006425',\n",
       " u'ref',\n",
       " u'NC_010314.1',\n",
       " u' Abaca bunchy top virus DNA-N, complete genome\\nAGCAGGGGGGCTTATTATTACCCCCCCTGCTCGGGGCGGGACATTCTGTGATGGGCTGGGCTTTATGCGG\\nCCAAATAAGCCCATAAAGCCAGATCTGGGCCCATTTAAGGGCCCGTGGTTTGAAAATGTCGCGTTCCCGC\\nCTAAATTGTTTGCTTGCCCTGCAAGGAAACGAAAACTCTATAAATAGGGTTGTTCTCTGCTTGTTTAATA\\nCATCAGGCGCAAATCTTTTGCAACGATGGATTGGATGGAATCACAATTCAAGACATGTACGCATGGCTGC\\nGACTGGAAGGCGATAGCTCCAGAAGCACAAGATAATATACAGGTAATTACATGTTCCGATTCAGGTTACG\\nGAAGAAAGAACCCTCGTAAGGTTCTTCTGAGGAGTATTCAGATAGGGTTCAATGGAAGCTTCAGAGGAAG\\nTAATAGAAATGTTCGAGGCTTCATATACGTGTCTGTAAGACAGGATGATGGCCAAATGAGACCAATTATG\\nGTCGTTCCATTCGGAGGGTATGGATATCATAACGACTACTATTATTTTGAAGGACAATCCAGTACGAATT\\nGTGAGATAGTGTCGGACTATATTCCGGCCGGTCAAGACTGGAGCAGAGATATGGAGATAAGTATAAGTAA\\nCAGCAACAATTGTAATCAAGAGTGCGATATCAAGTGTTATGTAGTATGTAATTTAAGAATTAAGGAATAA\\nWATTGTTGCCGAAGGTCTGTTATTTGAATGTTGAGATAAGGAAAGGGGCGGCGAAGCATGTGTGTATAAT\\nAACATATAACACACTATTATATATTTTGTAAAGAATAAAATTATGACCTGTCAGATTAAGTTTAGAATGA\\nACTGAGGCCGAAGGCCTCACCGAGGCCGAAGGCCGTCAGGATGGTTTTACAAAATAATTATAAGCACCTG\\nTACTAAGTACGAAGAGCGGTATAATATCTGAAAGGAAAAAATAATAATATAATAAAAATATTATGATGTC\\nCCAAAATAGCAGAATGCTAAAGGAACAAAAGGATGCTCTAAGTACAGGGTTGCGTGCTCTGGACGCCACT\\nTTAGTGGTGGGCCAGATGTCCCGAGTTAGTGCGCCACGTC\\n']"
      ]
     },
     "execution_count": 20,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "all = sc.union(rf)\n",
    "all.first()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  }
 ],
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  "kernelspec": {
   "display_name": "Python 2",
   "language": "python",
   "name": "python2"
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