Mercurial > repos > jankanis > blast2html

comparison blast2html.py @ 99:8f02008a5f20

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
look at all blast*.loc files; python2.6 compat fix
author Jan Kanis <jan.code@jankanis.nl>
date Tue, 01 Jul 2014 16:00:29 +0200
parents e780606b7c25
children 5bfaa3ee1f27
comparison
equal deleted inserted replaced
98:e780606b7c25 99:8f02008a5f20
14 import six, codecs 14 import six, codecs
15 from six.moves import builtins 15 from six.moves import builtins
16 from os import path 16 from os import path
17 from itertools import repeat 17 from itertools import repeat
18 from collections import defaultdict 18 from collections import defaultdict
19 import glob
19 import argparse 20 import argparse
20 from lxml import objectify 21 from lxml import objectify
21 import jinja2 22 import jinja2
22 23
23 builtin_str = str 24 builtin_str = str
372 link = template.format(**args) 373 link = template.format(**args)
373 except Exception as e: 374 except Exception as e:
374 warnings.warn('Error in formatting gene bank link {} with {}: {}'.format(template, args, e)) 375 warnings.warn('Error in formatting gene bank link {} with {}: {}'.format(template, args, e))
375 return text if display_nolink else '' 376 return text if display_nolink else ''
376 377
377 classattr = 'class="{}" '.format(jinja2.escape(clas)) if clas is not None else '' 378 classattr = 'class="{0}" '.format(jinja2.escape(clas)) if clas is not None else ''
378 return jinja2.Markup("<a {}href=\"{}\">{}</a>".format(classattr, jinja2.escape(link), jinja2.escape(text))) 379 return jinja2.Markup("<a {0}href=\"{1}\">{2}</a>".format(classattr, jinja2.escape(link), jinja2.escape(text)))
379 380
380 381
381 def read_genelinks(dir): 382 def read_genelinks(dir):
382 links = {} 383 links = {}
383 for f in ('blastdb.loc', 'blastdb_p.loc', 'blastdb_d.loc'): 384 # blastdb.loc, blastdb_p.loc, blastdb_d.loc, etc.
385 # sort reversed, so blastdb.loc will take precedence
386 for f in sorted(glob.glob(path.join(dir, 'blastdb*.loc')), reverse=True):
384 try: 387 try:
385 f = open(path.join(dir, f)) 388 f = open(path.join(dir, f))
386 for l in f.readlines(): 389 for l in f.readlines():
387 if l.strip().startswith('#'): 390 if l.strip().startswith('#'):
388 continue 391 continue