comparison prepare_amplicon_info.py @ 11:5671e1d3d5ee draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 8ce6fd9aee543d9e62db33a9c95f79d8dc4e6dea

10:9f978da6528a

# parse primers and their start positions from BED file
primer_starts = {}
with open(sys.argv[1]) as i:
    for line in i:
        f = line.strip().split('\t')
        try:
            if f[5] == '+':
                primer_starts[f[3]] = int(f[1])
            elif f[5] == '-':
                primer_starts[f[3]] = int(f[2]) - 1

# parse amplicon info and record outer primer names
with open(sys.argv[2]) as i:
    ret_lines = []
    for line in i:
        first = last = None
        for pname in line.strip().split('\t'):
            try:
                primer_start = primer_starts[pname]
            except KeyError:
                sys.exit(
                    'Amplicon info with primer name not found in '

11:5671e1d3d5ee

# parse primers and their start positions from BED file
primer_starts = {}
with open(sys.argv[1]) as i:
    for line in i:
        line = line.strip()
        if not line:
            continue
        f = line.split('\t')
        try:
            if f[5] == '+':
                primer_starts[f[3]] = int(f[1])
            elif f[5] == '-':
                primer_starts[f[3]] = int(f[2]) - 1

# parse amplicon info and record outer primer names
with open(sys.argv[2]) as i:
    ret_lines = []
    for line in i:
        line = line.strip()
        if not line:
            continue
        first = last = None
        for pname in line.split('\t'):
            try:
                primer_start = primer_starts[pname]
            except KeyError:
                sys.exit(
                    'Amplicon info with primer name not found in '