probeRC.py 文件源码

def createRCs(inputFile, outNameVal):
    """Creates a .bed file with the reverse complements of the given set of
    sequences."""

    # Determine the stem of the input filename.
    fileName = str(inputFile).split('.')[0]

    # Open input file for reading.
    with open(inputFile, 'r') as f:
        file_read = [line.strip() for line in f]

    # Create list to hold output.
    outList = []

    # Parse out probe info, flip sequence to RC, and write to output list.
    for i in range(0, len(file_read), 1):
        chrom = file_read[i].split('\t')[0]
        start = file_read[i].split('\t')[1]
        stop = file_read[i].split('\t')[2]
        probeSeq = file_read[i].split('\t')[3]
        RevSeq = Seq(probeSeq, IUPAC.unambiguous_dna).reverse_complement()
        Tm = file_read[i].split('\t')[4]
        outList.append('%s\t%s\t%s\t%s\t%s' % (chrom, start, stop, RevSeq, Tm))

    # Determine the name of the output file.
    if outNameVal is None:
        outName = '%s_RC' % fileName
    else:
        outName = outNameVal

    # Create the output file.
    output = open('%s.bed' % outName, 'w')

    # Write the output file
    output.write('\n'.join(outList))
    output.close()