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A new version of ngsfilger without a bug about error count between primers and sequence

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This commit is contained in:
Eric Coissac
2012-08-20 17:00:50 +00:00
parent 0c001ae0be
commit baa5b51c5b
1 changed files with 8 additions and 4 deletions
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12
src/ngsfilter.py
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@ -356,14 +356,16 @@ def annotate(sequence,options):
sequence['tail_quality']=q sequence['tail_quality']=q
primers = options.primers primers = options.primers
print >>sys.stderr,"directmatch" if options.debug:
print >>sys.stderr,"directmatch"
directmatch = [(p,p(sequence)) for p in primers] directmatch = [(p,p(sequence)) for p in primers]
directmatch.sort(cmp=sortMatch) directmatch.sort(cmp=sortMatch)
directmatch=directmatch[0] if directmatch[0][1] is not None else None directmatch=directmatch[0] if directmatch[0][1] is not None else None
print >>sys.stderr,">>>>",directmatch if options.debug:
print >>sys.stderr,">>>>",directmatch
if directmatch is None: if directmatch is None:
sequence['error']='No primer match' sequence['error']='No primer match'
return False,sequence return False,sequence
@ -389,12 +391,14 @@ def annotate(sequence,options):
del sequence['cut'] del sequence['cut']
primers = options.primers[directmatch[0]] primers = options.primers[directmatch[0]]
print >>sys.stderr,"reverse match" if options.debug:
print >>sys.stderr,"reverse match"
reversematch = [(p,p(sequence)) for p in primers if p is not None] reversematch = [(p,p(sequence)) for p in primers if p is not None]
reversematch.sort(cmp=sortMatch) reversematch.sort(cmp=sortMatch)
reversematch = reversematch[0] if reversematch[0][1] is not None else None reversematch = reversematch[0] if reversematch[0][1] is not None else None
print >>sys.stderr,"<<<<",reversematch if options.debug:
print >>sys.stderr,"<<<<",reversematch
if reversematch is None and None not in primers: if reversematch is None and None not in primers:
if directmatch[0].direct: if directmatch[0].direct:
message = 'No reverse primer match' message = 'No reverse primer match'