comparison xmfa2gff3.py @ 1:bca52822843e draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit e0cd7ae10ce97bed51594e7cc0b969a803d698b7

0:74093fb62bdf

#!/usr/bin/env python
import sys
from Bio import SeqIO
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from Bio.SeqFeature import SeqFeature, FeatureLocation
import argparse
from BCBio import GFF
import logging
logging.basicConfig(level=logging.INFO)
log = logging.getLogger(__name__)


def parse_xmfa(xmfa):

            for other in others:
                pid = _percent_identity(block_seq, other['seq'][i:i + real_window_size])
                # Ignore 0% identity sequences
                if pid == 0:
                    continue
                other['feature'].sub_features.append(
                    SeqFeature(
                        FeatureLocation(real_start, real_end),
                        type="match_part", strand=strand,
                        qualifiers={

1:bca52822843e

#!/usr/bin/env python
import argparse
import logging
import sys

from BCBio import GFF
from Bio import SeqIO
from Bio.Seq import Seq
from Bio.SeqFeature import (
    FeatureLocation,
    SeqFeature
)
from Bio.SeqRecord import SeqRecord

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


def parse_xmfa(xmfa):

            for other in others:
                pid = _percent_identity(block_seq, other['seq'][i:i + real_window_size])
                # Ignore 0% identity sequences
                if pid == 0:
                    continue

                # Support for Biopython 1.68 and above, which removed sub_features
                if not hasattr(other['feature'], "sub_features"):
                    other['feature'].sub_features = []
                other['feature'].sub_features.append(
                    SeqFeature(
                        FeatureLocation(real_start, real_end),
                        type="match_part", strand=strand,
                        qualifiers={