Commit 117487ad authored by Alisa Muraveva's avatar Alisa Muraveva
Browse files

It partially works with strange coordinates (with links to other reference)

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/mobile-2013@737 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
parent d774c18f
......@@ -129,8 +129,7 @@ class EMBLparser():
for i in locationList.sub_features :
if i.ref : # This is a workaround for a bug in BioPython.
ret = None
break
return None
#if
temp = self.__location2pos(i.location)
if temp :
......@@ -626,7 +625,7 @@ class EMBLparser():
myTranscript = Locus(myRealGene.newLocusTag())
myTranscript.mRNA = PList()
myTranscript.mRNA.positionList = i.positionList
myTranscript.mRNA.location = [i.positionList[0], i.positionList[-1]]
myTranscript.mRNA.location = [i.positionList[0], i.positionList[-1]] if i.positionList else None
myTranscript.transcribe = True
myTranscript.transcriptID = i.transcript_id
myTranscript.transcriptProduct = i.product
......@@ -635,7 +634,7 @@ class EMBLparser():
if i.link :
myTranscript.CDS = PList()
myTranscript.CDS.positionList = i.link.positionList
myTranscript.CDS.location = [i.link.positionList[0], i.link.positionList[-1]]
myTranscript.CDS.location = [i.link.positionList[0], i.link.positionList[-1]]if i.positionList else None
myTranscript.translate = True
myTranscript.proteinID = i.link.protein_id
myTranscript.linkMethod = i.linkMethod
......@@ -681,7 +680,7 @@ class EMBLparser():
myTranscript = Locus(myRealGene.newLocusTag())
myTranscript.CDS = PList()
myTranscript.CDS.positionList = i.positionList
myTranscript.CDS.location = [i.positionList[0], i.positionList[-1]]
myTranscript.CDS.location = [i.positionList[0], i.positionList[-1]] if i.positionList else None
myTranscript.proteinID = i.protein_id
myTranscript.proteinProduct = i.product
if i.qualifiers.has_key("transl_table") :
......
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