comparison ete_lineage_generator.py @ 4:87b6de3ef63e draft

planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 41e40314a9b25a9f3c06a13422d367b68334f593

3:077021c45b96

# check command line options
if options.input_species_filename is None:
    parser.error("-s option must be specified, Species list in text format one species in each line")
if options.full and options.ranks:
    parser.error("-f and -r can not be used at the same time")
if options.ranks:
    for r in options.ranks:
        if r not in LONG_RANKS:
            parser.error("unknown rank %s" % r)
# setup output

if options.compress:
    for ir in range(len(RANKS)):
        for ilr in range(len(LONG_RANKS)):
            if RANKS[ir] in LONG_RANKS[ilr]:
                COMP_RANK_IDX[LONG_RANKS[ilr]] = ir
with open(options.input_species_filename) as f:
    for line in f.readlines():
        line = line.strip().replace('_', ' ')
        try:
            taxid = int(line)

4:87b6de3ef63e

# check command line options
if options.input_species_filename is None:
    parser.error("-s option must be specified, Species list in text format one species in each line")
if options.full and options.ranks:
    parser.error("-f and -r can not be used at the same time")

if options.ranks:
    for r in options.ranks:
        if r not in LONG_RANKS:
            parser.error("unknown rank %s" % r)
# setup output

if options.compress:
    for ir in range(len(RANKS)):
        for ilr in range(len(LONG_RANKS)):
            if RANKS[ir] in LONG_RANKS[ilr]:
                COMP_RANK_IDX[LONG_RANKS[ilr]] = ir
# write header
of.write("#species/taxid\t%s\n" % ("\t".join(RANKS)))
# get and write data
with open(options.input_species_filename) as f:
    for line in f.readlines():
        line = line.strip().replace('_', ' ')
        try:
            taxid = int(line)