comparison tools/effectiveT3/effectiveT3.py @ 24:a3d660e900b1 draft

planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 commit 7a746d55f0e8456992ee11c49a507285f9f39383-dirty

23:69ab4d862db2

model, threshold, fasta_file, tabular_file = sys.argv[1:]

if not os.path.isfile(fasta_file):
    sys.exit("Input FASTA file not found: %s" % fasta_file)

if threshold not in ["selective", "sensitive"] \
    and not threshold.startswith("cutoff="):
    sys.exit("Threshold should be selective, sensitive, or cutoff=..., not %r" % threshold)


def clean_tabular(raw_handle, out_handle):
    """Clean up Effective T3 output to make it tabular."""
    count = 0
    positive = 0
    errors = 0
    for line in raw_handle:
        if not line or line.startswith("#") \
            or line.startswith("Id; Description; Score;"):
            continue
        assert line.count(";") >= 3, repr(line)
        # Normally there will just be three semi-colons, however the
        # original FASTA file's ID or description might have had
        # semi-colons in it as well, hence the following hackery:

24:a3d660e900b1

model, threshold, fasta_file, tabular_file = sys.argv[1:]

if not os.path.isfile(fasta_file):
    sys.exit("Input FASTA file not found: %s" % fasta_file)

if threshold not in ["selective", "sensitive"] and not threshold.startswith("cutoff="):
    sys.exit("Threshold should be selective, sensitive, or cutoff=..., not %r" % threshold)


def clean_tabular(raw_handle, out_handle):
    """Clean up Effective T3 output to make it tabular."""
    count = 0
    positive = 0
    errors = 0
    for line in raw_handle:
        if not line or line.startswith("#") or line.startswith("Id; Description; Score;"):
            continue
        assert line.count(";") >= 3, repr(line)
        # Normally there will just be three semi-colons, however the
        # original FASTA file's ID or description might have had
        # semi-colons in it as well, hence the following hackery: