Package obitools :: Package tagmatcher
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Source Code for Package obitools.tagmatcher

 1  from obitools import NucSequence 
 2  from obitools.location import locationGenerator,extractExternalRefs 
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6 -class TagMatcherSequence(NucSequence):
7 ''' 8 Class used to represent a nucleic sequence issued mapped 9 on a genome by the tagMatcher software. 10 ''' 11
12 - def __init__(self,seq,cd,locs,dm,rm):
13 NucSequence.__init__(self, seq, seq) 14 self['locations']=locs 15 self['conditions']=cd 16 self['dm']=dm 17 self['rm']=rm 18 self['tm']=dm+rm
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20 - def eminEmaxFilter(self,emin=None,emax=None):
21 result = [x for x in self['locations'] 22 if (emin is None or x['error'] >=emin) 23 and (emax is None or x['error'] <=emax)] 24 self['locations']=result 25 dm=0 26 rm=0 27 for x in result: 28 if x.isDirect(): 29 dm+=1 30 else: 31 rm+=1 32 self['dm']=dm 33 self['rm']=rm 34 self['tm']=dm+rm 35 return self
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