makeMicroarrayMatrix.py

import glob

# Get a list of the '.clone' files in the 
files = glob.glob('*.clone')

# Read in expression data and put it into a dictionary
matrixDictionary = {}
conditions = []
for file in files:
    condition = file.split('.')[0]
    conditions.append(condition)
    inFile = open(file,'r')
    print inFile.readline().strip().split('\t')[297] # Get rid of header
    while 1:
        line = inFile.readline()
        if not line:
            break
        splitUp = line.strip().split('\t')
        if not splitUp[0] in matrixDictionary:
            matrixDictionary[splitUp[0]] = {}
        matrixDictionary[splitUp[0]][condition] = splitUp[297]
    inFile.close()

# Turn dictionary into matrix file for import into R
outFile = open('ffrpValidation.csv','w')
outFile.write(','+','.join(conditions))
for locus in matrixDictionary:
    outFile.write('\n'+locus+','+','.join([matrixDictionary[locus][c] for c in conditions]))
outFile.close()