comparison mut2read.py @ 1:3556001ff2db draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 60dc8db809909edf44d662683b1f392b9d5964bf"

0:8d29173d49a9

    if os.path.isfile(file3) is False:
        sys.exit("Error: Could not find '{}'".format(file3))

    # read mut file
    with open(file1, 'r') as mut:
        mut_array = np.genfromtxt(mut, skip_header=1, delimiter='\t', comments='#', dtype='string')

    # read dcs bam file
    # pysam.index(file2)
    bam = pysam.AlignmentFile(file2, "rb")

        ref = mut_array[m, 9]
        alt = mut_array[m, 10]

        dcs_len = []

        for pileupcolumn in bam.pileup(chrom.tobytes(), stop_pos - 2, stop_pos, max_depth=100000000):

            if pileupcolumn.reference_pos == stop_pos - 1:
                count_alt = 0
                count_ref = 0
                count_indel = 0

1:3556001ff2db

    if os.path.isfile(file3) is False:
        sys.exit("Error: Could not find '{}'".format(file3))

    # read mut file
    with open(file1, 'r') as mut:
        mut_array = np.genfromtxt(mut, skip_header=1, delimiter='\t', comments='#', dtype=str)

    # read dcs bam file
    # pysam.index(file2)
    bam = pysam.AlignmentFile(file2, "rb")

        ref = mut_array[m, 9]
        alt = mut_array[m, 10]

        dcs_len = []

        for pileupcolumn in bam.pileup(chrom, stop_pos - 2, stop_pos, max_depth=100000000):

            if pileupcolumn.reference_pos == stop_pos - 1:
                count_alt = 0
                count_ref = 0
                count_indel = 0