Mercurial > repos > iuc > jbrowse

comparison blastxml_to_gapped_gff3.py @ 8:ad4b9d7eae6a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
author iuc
date Tue, 29 Nov 2016 10:55:30 -0500
parents 7342f467507b
children db5fe5a3176a
comparison
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7:1e74f16adaa1 8:ad4b9d7eae6a
1 #!/usr/bin/perl 1 #!/usr/bin/perl
2 import argparse
3 import copy
4 import logging
2 import re 5 import re
3 import sys 6 import sys
4 import copy 7
5 import argparse
6 from BCBio import GFF 8 from BCBio import GFF
7 import logging 9
8 logging.basicConfig(level=logging.INFO) 10 logging.basicConfig(level=logging.INFO)
9 log = logging.getLogger(name='blastxml2gff3') 11 log = logging.getLogger(name='blastxml2gff3')
10 12
11 __author__ = "Eric Rasche" 13 __author__ = "Eric Rasche"
12 __version__ = "0.4.0" 14 __version__ = "0.4.0"
216 else: 218 else:
217 ret = 'X' 219 ret = 'X'
218 else: 220 else:
219 log.warn("Bad data: \n\t%s\n\t%s\n\t%s\n" % (query, match, subject)) 221 log.warn("Bad data: \n\t%s\n\t%s\n\t%s\n" % (query, match, subject))
220 222
221
222 if strict_m: 223 if strict_m:
223 if ret == '=' or ret == 'X': 224 if ret == '=' or ret == 'X':
224 ret = 'M' 225 ret = 'M'
225 226
226 matchline.append(ret) 227 matchline.append(ret)