comparison xmfa2gff3.py @ 3:97a43bcbf44d draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit fc61c9d4850614a6580d25f92e3032dc8edbc10d"

2:bdb752f3c6bb

)
from Bio.SeqRecord import SeqRecord

logging.basicConfig(level=logging.INFO)
log = logging.getLogger(__name__)


def parse_xmfa(xmfa):
    """Simple XMFA parser until https://github.com/biopython/biopython/pull/544
    """

            other['feature'] = SeqFeature(
                FeatureLocation(parent['start'], parent['end'] + 1),
                type="match", strand=parent['strand'],
                qualifiers={
                    "source": "progressiveMauve",
                    "target": label_convert.get(other['id'], other['id']),
                    "ID": label_convert.get(other['id'], 'xmfa_' + other['rid'])
                }
            )

        for i in range(0, len(lcb[0]['seq']), window_size):

    return records


if __name__ == '__main__':
    parser = argparse.ArgumentParser(description='Convert XMFA alignments to gff3', prog='xmfa2gff3')
    parser.add_argument('xmfa_file', type=file, help='XMFA File')
    parser.add_argument('--window_size', type=int, help='Window size for analysis', default=1000)
    parser.add_argument('--relative_to', type=str, help='Index of the parent sequence in the MSA', default='1')
    parser.add_argument('--sequences', type=file, nargs='+',
                        help='Fasta files (in same order) passed to parent for reconstructing proper IDs')
    parser.add_argument('--version', action='version', version='%(prog)s 1.0')

    args = parser.parse_args()

3:97a43bcbf44d

)
from Bio.SeqRecord import SeqRecord

logging.basicConfig(level=logging.INFO)
log = logging.getLogger(__name__)


# Patch bcbio gff to work around url encoding issue. This is clearly
# sub-optimal but we should transition to the newer library.
def _new_format_keyvals(self, keyvals):
    return ";".join(["%s=%s" % (k, ",".join(v)) for (k, v) in sorted(keyvals.items())])


GFF.GFFOutput.GFF3Writer._format_keyvals = _new_format_keyvals


def parse_xmfa(xmfa):
    """Simple XMFA parser until https://github.com/biopython/biopython/pull/544
    """

            other['feature'] = SeqFeature(
                FeatureLocation(parent['start'], parent['end'] + 1),
                type="match", strand=parent['strand'],
                qualifiers={
                    "source": "progressiveMauve",
                    "Target": " ".join(map(str, [label_convert.get(other['id'], other['id']), other['start'], other['end'], '+' if other['strand'] > 0 else '-'])),
                    "ID": label_convert.get(other['id'], 'xmfa_' + other['rid'])
                }
            )

        for i in range(0, len(lcb[0]['seq']), window_size):

    return records


if __name__ == '__main__':
    parser = argparse.ArgumentParser(description='Convert XMFA alignments to gff3', prog='xmfa2gff3')
    parser.add_argument('xmfa_file', type=argparse.FileType('r'), help='XMFA File')
    parser.add_argument('--window_size', type=int, help='Window size for analysis', default=1000)
    parser.add_argument('--relative_to', type=str, help='Index of the parent sequence in the MSA', default='1')
    parser.add_argument('--sequences', type=argparse.FileType('r'), nargs='+',
                        help='Fasta files (in same order) passed to parent for reconstructing proper IDs')
    parser.add_argument('--version', action='version', version='%(prog)s 1.0')

    args = parser.parse_args()