Mercurial > repos > iuc > progressivemauve
comparison xmfa2gff3.py @ 1:bca52822843e draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit e0cd7ae10ce97bed51594e7cc0b969a803d698b7
author | iuc |
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date | Fri, 07 Sep 2018 11:30:11 -0400 |
parents | 74093fb62bdf |
children | 97a43bcbf44d |
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0:74093fb62bdf | 1:bca52822843e |
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1 #!/usr/bin/env python | 1 #!/usr/bin/env python |
2 import argparse | |
3 import logging | |
2 import sys | 4 import sys |
5 | |
6 from BCBio import GFF | |
3 from Bio import SeqIO | 7 from Bio import SeqIO |
4 from Bio.Seq import Seq | 8 from Bio.Seq import Seq |
9 from Bio.SeqFeature import ( | |
10 FeatureLocation, | |
11 SeqFeature | |
12 ) | |
5 from Bio.SeqRecord import SeqRecord | 13 from Bio.SeqRecord import SeqRecord |
6 from Bio.SeqFeature import SeqFeature, FeatureLocation | 14 |
7 import argparse | |
8 from BCBio import GFF | |
9 import logging | |
10 logging.basicConfig(level=logging.INFO) | 15 logging.basicConfig(level=logging.INFO) |
11 log = logging.getLogger(__name__) | 16 log = logging.getLogger(__name__) |
12 | 17 |
13 | 18 |
14 def parse_xmfa(xmfa): | 19 def parse_xmfa(xmfa): |
129 for other in others: | 134 for other in others: |
130 pid = _percent_identity(block_seq, other['seq'][i:i + real_window_size]) | 135 pid = _percent_identity(block_seq, other['seq'][i:i + real_window_size]) |
131 # Ignore 0% identity sequences | 136 # Ignore 0% identity sequences |
132 if pid == 0: | 137 if pid == 0: |
133 continue | 138 continue |
139 | |
140 # Support for Biopython 1.68 and above, which removed sub_features | |
141 if not hasattr(other['feature'], "sub_features"): | |
142 other['feature'].sub_features = [] | |
134 other['feature'].sub_features.append( | 143 other['feature'].sub_features.append( |
135 SeqFeature( | 144 SeqFeature( |
136 FeatureLocation(real_start, real_end), | 145 FeatureLocation(real_start, real_end), |
137 type="match_part", strand=strand, | 146 type="match_part", strand=strand, |
138 qualifiers={ | 147 qualifiers={ |