comparison seg2matrix/segToMatrixGalaxy.py @ 54:59dbe857f5d4

introduce normal_CNV parameter

53:7de3db823f90

        self.chrom_end = chrom_end
        self.strand = "."


if __name__ == "__main__":
    if len(sys.argv[:])!= 5:
        print "python segToMatrixGalaxy.py inputSegmentFile refGeneFile outputMatrix outputProbeMap\n"
        sys.exit()
    seg = CGData.GenomicSegment.GenomicSegment()
    seg.load(sys.argv[1])
    
    refgene = CGData.RefGene.RefGene()
    refgene.load(sys.argv[2])
#    refgene.load(os.path.dirname(sys.argv[0])+"/"+sys.argv[2])

    handle = open(sys.argv[3], "w")
    m = matrix_write(handle)    
    CGData.SegToMatrix.seg_to_matrix(seg, m)
    handle.close()
    
    handle = open(sys.argv[4], "w")
    probeMapper = CGData.GeneMap.ProbeMapper('b')
    handle.write("%s\t%s\t%s\t%s\t%s\t%s\n" % ("#id", "gene","chrom","chromStart","chromEnd","strand"))
    for probe in m.probes:
        hits = []
        for hit in probeMapper.find_overlap( probe, refgene ):
            if hit.name not in hits:
                hits.append(hit.name)

54:59dbe857f5d4

        self.chrom_end = chrom_end
        self.strand = "."


if __name__ == "__main__":
    if len(sys.argv[:])!= 6:
        print "python segToMatrixGalaxy.py inputSegmentFile refGeneFile outputMatrix outputProbeMap NORMAL_CNV\n"
        sys.exit()
    seg = CGData.GenomicSegment.GenomicSegment()
    seg.load(sys.argv[1])
    
    refgene = CGData.RefGene.RefGene()
    refgene.load(os.path.dirname(sys.argv[0])+"/"+os.path.basename(sys.argv[2]))

    NORMAL_CNV = sys.argv[5]

    handle = open(sys.argv[3], "w")
    m = matrix_write(handle)    
    CGData.SegToMatrix.seg_to_matrix(seg, m, NORMAL_CNV)
    handle.close()
    
    handle = open(sys.argv[4], "w")
    probeMapper = CGData.GeneMap.ProbeMapper('b')
    handle.write("%s\t%s\t%s\t%s\t%s\t%s\n" % ("id", "gene","chrom","chromStart","chromEnd","strand"))
    for probe in m.probes:
        hits = []
        for hit in probeMapper.find_overlap( probe, refgene ):
            if hit.name not in hits:
                hits.append(hit.name)