Mercurial > repos > jankanis > blast2html

comparison blast2html.py @ 101:5bfaa3ee1f27

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better warning message
author Jan Kanis <jan.code@jankanis.nl>
date Tue, 01 Jul 2014 16:51:38 +0200
parents 8f02008a5f20
children 87c5402e0ba8
comparison
equal deleted inserted replaced
100:be7c94e29cd8 101:5bfaa3ee1f27
380 380
381 381
382 def read_genelinks(dir): 382 def read_genelinks(dir):
383 links = {} 383 links = {}
384 # blastdb.loc, blastdb_p.loc, blastdb_d.loc, etc. 384 # blastdb.loc, blastdb_p.loc, blastdb_d.loc, etc.
385 # sort reversed, so blastdb.loc will take precedence 385 files = sorted(glob.glob(path.join(dir, 'blastdb*.loc')))
386 for f in sorted(glob.glob(path.join(dir, 'blastdb*.loc')), reverse=True): 386 # reversed, so blastdb.loc will take precedence
387 for f in reversed(files):
387 try: 388 try:
388 f = open(path.join(dir, f)) 389 f = open(path.join(dir, f))
389 for l in f.readlines(): 390 for l in f.readlines():
390 if l.strip().startswith('#'): 391 if l.strip().startswith('#'):
391 continue 392 continue
396 continue 397 continue
397 f.close() 398 f.close()
398 except OSError: 399 except OSError:
399 continue 400 continue
400 if not links: 401 if not links:
401 warnings.warn("No gene bank link templates found") 402 warnings.warn("No gene bank link templates found in {0}".format(', '.join(files))
402 return links 403 return links
403 404
404 405
405 def main(): 406 def main():
406 default_template = path.join(path.dirname(__file__), 'blast2html.html.jinja') 407 default_template = path.join(path.dirname(__file__), 'blast2html.html.jinja')