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Add management of quality scores

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Eric Coissac
2010-04-01 20:01:02 +00:00
parent 5a45fae59b
commit 96a3b0ba00
1 changed files with 6 additions and 0 deletions
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6
src/obitools/__init__.py
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@@ -474,6 +474,9 @@ class SubSequence(WrappedBioSequence):
self._info['cut']='[%d,%d,%s]' % self._indices self._info['cut']='[%d,%d,%s]' % self._indices
self._eval['cut']=True self._eval['cut']=True
if hasattr(reference,'quality'):
self.quality = reference.quality[self._location]
def getId(self): def getId(self):
d = self._id or ("%s_SUB" % self.wrapped.id) d = self._id or ("%s_SUB" % self.wrapped.id)
return d return d
@@ -523,6 +526,9 @@ class DNAComplementSequence(WrappedBioSequence):
assert reference.isNucleotide() assert reference.isNucleotide()
self._info['complemented']=True self._info['complemented']=True
self._eval['complemented']=True self._eval['complemented']=True
if hasattr(reference,'quality'):
self.quality = reference.quality[::-1]
def getId(self): def getId(self):
d = self._id or ("%s_CMP" % self.wrapped.id) d = self._id or ("%s_CMP" % self.wrapped.id)