comparison mergeGenomicMatrixFiles.py @ 7:1d150e860c4d

Expanded the functionality of the merge genomic datasets tool, to generate an output dataset with the file (or label) indicating where each column came from

6:2035405538b4

#!/usr/bin/env python

import string,os,sys

def header (samples, infile):
    fin= open(infile,'r')
    #header, samples
    newSamples = string.split(string.strip(fin.readline()),'\t')[1:]
    for sample in newSamples:
        if sample not in samples:
            samples[sample]= len(samples)
    fin.close()
    return

def process(genes, samples, dataMatrix, infile):
    maxLength= len(samples)

            dataMatrix[x][y]= data[i]

    fin.close()
    return

def outputMatrix(dataMatrix, samples, genes, outfile):
    fout = open(outfile,"w")
    maxLength= len(samples)
    sList=[]
    for i in range (0, maxLength):
        sList.append("")

        fout.write("\n")
    fout.close()
    return

if __name__ == '__main__' :
    if len(sys.argv[:]) <4:
        print "python mergeFilesByColumn.py output inputfile(s)"
        print "**********memory intensive, not for very genomic data with hugo number of probes"
        print "this is merging data A+B=C\n"
        sys.exit()

    inFiles = sys.argv[2:]
    outfile = sys.argv[1]

    genes={}
    samples={}
    dataMatrix=[]

    for infile in inFiles:
        header (samples, infile)

    for infile in inFiles:
        process(genes, samples, dataMatrix, infile)

    outputMatrix(dataMatrix, samples, genes, outfile)

7:1d150e860c4d

#!/usr/bin/env python

import argparse
import string,os,sys

def header (samples, sourceFiles, infile, labelThisFile):
    if labelThisFile == None:
        labelToUse = infile
    else:
        labelToUse = labelThisFile
    fin= open(infile,'r')
    #header, samples
    newSamples = string.split(string.strip(fin.readline()),'\t')[1:]
    for sample in newSamples:
        if sample not in samples:
            samples[sample]= len(samples)
            sourceFiles[sample] = labelToUse
    fin.close()
    return

def process(genes, samples, dataMatrix, infile):
    maxLength= len(samples)

            dataMatrix[x][y]= data[i]

    fin.close()
    return


def outputSourceMatrix(sourceData, outputFileName):
    fout = open(outputFileName, "w")
    fout.write("Sample\tSource\n")
    for thisSample in sourceData.keys():
        fout.write("%s\t%s\n" % (thisSample, sourceData[thisSample]))
    fout.close()
    return


def outputMergedMatrix(dataMatrix, samples, genes, outfile):
    fout = open(outfile,"w")
    maxLength= len(samples)
    sList=[]
    for i in range (0, maxLength):
        sList.append("")

        fout.write("\n")
    fout.close()
    return

if __name__ == '__main__' :
    #
    # The input files to this script are two or more matrices, in which
    # columns represent samples and rows represent genes or measurements.
    # There are two output files: outMergedData contains the input data merged
    # into a single matrix, and outSourceMatrix is a two-column matrix 
    # indicating which file each sample (or column label) came from.  This
    # assumes that each sample came from at most one file.
    #
    parser = argparse.ArgumentParser()
    parser.add_argument("inFileA", type=str, help="First input file")
    parser.add_argument("inFileB", type=str, help="Second input file")
    parser.add_argument("outMergedData", type=str, 
                        help="Filename for the merged dataset")
    parser.add_argument("outSourceMatrix", type=str,
                        help="""Filename for a Nx2 matrix that indicates
                                the source file of each column""")
    parser.add_argument("--aLabel", type=str, default=None,
                        help="User-friendly label for the first input file")
    parser.add_argument("--bLabel", type=str, default=None,
                        help="User-friendly label for the second input file")
    args = parser.parse_args()
    outSourceMatrix = sys.argv[2]  

    genes={}
    samples={}
    sourceFiles = {}
    dataMatrix=[]

    header(samples, sourceFiles, args.inFileA, args.aLabel)
    header(samples, sourceFiles, args.inFileB, args.bLabel)

    process(genes, samples, dataMatrix, args.inFileA)
    process(genes, samples, dataMatrix, args.inFileB)

    outputSourceMatrix(sourceFiles, args.outSourceMatrix)
    outputMergedMatrix(dataMatrix, samples, genes, args.outMergedData)