Converting Files from htseq-count to Matrix

makeTable.py

from subprocess import *
from shutil import move
import os

# Read in manifest of samples to process
samples = []
inFile = open('manifest.csv','r')
while 1:
    line = inFile.readline()
    if not line:
        break
    splitUp = line.strip().split(',')
    samples.append(splitUp[0])
inFile.close()

# Read in all *.transcripts.gtf files
gexpMatrix = {} # gexpMatrix[transcript][sample] = {'coverage':<>, 'FPKM':<>}
for sample in samples:
    print 'Reading',sample,'...'
    inFile = open('output/'+sample+'Aligned.out.counts','r')
    while 1:
        line = inFile.readline()
        if not line:
            break
        splitUp = line.strip().split('\t')
        if not splitUp[0] in gexpMatrix:
            gexpMatrix[splitUp[0]] = {}
        gexpMatrix[splitUp[0]][sample] = splitUp[1]
    inFile.close()
print 'Done reading files.'

print 'Starting writing coverage...'
# Dump out matrix of coverages
outFile = open('output/gexp_counts.csv','w')
outFile.write('UCSC_transcript_id,'+','.join(samples)+'\n')
outFile.write('\n'.join([transcript+','+','.join([gexpMatrix[transcript][sample] for sample in samples]) for transcript in gexpMatrix]))
outFile.close()

print 'Done.'