comparison convert_mga.py @ 1:17c7ab82bfbc draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit f66aa9a65aaf45ac4888ca26f5af661f73b46fdc

0:b04960a7abf5

            'seq_id', 'seq_model', 'seq_gc', 'seq_rbs',
            'gene ID', 'start pos', 'end pos', 'strand', 'frame',
            'complete/partial', 'gene score', 'used model',
            'rbs start', 'rbs end', 'rbs score']))

    gc_rbs_pat = '# gc = (-?[0-9]*[.]?[0-9]+), rbs = (-?[0-9]*[.]?[0-9]+)' 
    seq_count = 0
    gene_count = 0
    for i, line in enumerate(input_rdr):
        # 1317/1
        # gc = 0.272955, rbs = -1
        # self: -
        if line.startswith('# gc'):
            try:
                m = re.match(gc_rbs_pat, line.strip())
                seq_gc, seq_rbs = m.groups()
            except:
                seq_gc = seq_rbs = ''
        elif line.startswith('# self:'):
            seq_type = re.sub('# self:', '', line.rstrip())
        elif line.startswith('# '):
            seq_name = re.sub('# (\S+).*$', '\\1', line.rstrip())
            seq_count += 1
        else:
            fields = line.split('\t')
            if len(fields) == 11:
                gene_count += 1

1:17c7ab82bfbc

            'seq_id', 'seq_model', 'seq_gc', 'seq_rbs',
            'gene ID', 'start pos', 'end pos', 'strand', 'frame',
            'complete/partial', 'gene score', 'used model',
            'rbs start', 'rbs end', 'rbs score']))

    gc_rbs_pat = '# gc = (-?[0-9]*[.]?[0-9]+), rbs = (-?[0-9]*[.]?[0-9]+)'
    seq_count = 0
    gene_count = 0
    for i, line in enumerate(input_rdr):
        # 1317/1
        # gc = 0.272955, rbs = -1
        # self: -
        if line.startswith('# gc'):
            try:
                m = re.match(gc_rbs_pat, line.strip())
                seq_gc, seq_rbs = m.groups()
            except ValueError:
                seq_gc = seq_rbs = ''
        elif line.startswith('# self:'):
            seq_type = re.sub('# self:', '', line.rstrip())
        elif line.startswith('# '):
            seq_name = re.sub(r'# (\S+).*$', '\\1', line.rstrip())
            seq_count += 1
        else:
            fields = line.split('\t')
            if len(fields) == 11:
                gene_count += 1