pubExpMatrix

#!/usr/bin/env python

# load default python packages
import logging, optparse, sys, os
from os.path import *

# add <scriptDir>/lib/ to package search path
sys.path.insert(0, join(dirname(abspath(__file__)), "lib"))

import pubGeneric, pubExpMatrix, pubConf

def main(args, options):
    datasetStr, wordListFname, outBase = args
    dirNames = pubGeneric.resolveDatasetDesc(datasetStr)
    pubGeneric.setupLogging(__file__, options)
    wordListFname = join(os.getcwd(),wordListFname)
    posPmidFname = options.posPmids
    negPmidFname = options.negPmids
    assert(posPmidFname or negPmidFname) # need at least -p or -n
        
    if not isfile(wordListFname):
        logging.info("%s not found" % wordListFname)
        pubExpMatrix.buildWordList(inDirs, skipMap)
        logging.info("raw word list created, use your own command now to reduce it to something smaller")
        logging.info("e.g. cat wordFreq.tab | gawk '($2<50000) && ($2>100)' | cut -f1 | lstOp remove stdin /hive/data/outside/pubs/wordFrequency/google-ngrams/fiction/top100k.tab  | lstOp remove stdin /hive/data/outside/pubs/wordFrequency/bnc/bnc.txt > wordList.txt")
    else:
        pubExpMatrix.runMatrixJobs(outBase, dirNames, wordListFname, posPmidFname, negPmidFname, \
            options.skipMap, options.format, options.test)


# === COMMAND LINE INTERFACE, OPTIONS AND HELP ===
parser = optparse.OptionParser("""usage: %prog [options] datasets wordListFname outBasename - create an input file for svm light, mallet or weka. If wordListFname does not exist, it will be created. Need to specify at least -p or -n""")

parser.add_option("-d", "--debug", dest="debug", action="store_true", help="show debug messages")
parser.add_option("-v", "--verbose", dest="verbose", action="store_true", help="show more debug messages")
parser.add_option("", "--skipMap", dest="skipMap", action="store_true", help="skip map step")
#parser.add_option("-s", "--wordList", dest="wordList", action="store", help="optional list of words to use")
parser.add_option("-f", "--format", dest="format", action="store", help="output format, either svml or arff, default %default", default="arff")
parser.add_option("-p", "--posPmids", dest="posPmids", action="store", help="file with list of positive PMIDs")
parser.add_option("-n", "--negPmids", dest="negPmids", action="store", help="file with list of negative PMIDs")
parser.add_option("-t", "--test", dest="test", action="store_true", help="only run the test, nothing else")
(options, args) = parser.parse_args()

if args==[]:
    parser.print_help()
    exit(1)

main(args, options)