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Bug fix: fix warning for synonymous variants #10

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Bug fix: fix warning for synonymous variants #10

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4 changes: 3 additions & 1 deletion biomine/variant/mafvariant.py
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Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
import re
from biomine.variant.variant import variant
from urllib2 import unquote

class mafvariant(variant):
nonCoding = re.compile( "([NULL|\*|\+|\-])" )
Expand Down Expand Up @@ -260,6 +261,7 @@ def HGVSp( self ):
return hgvsp
def splitHGVSp( self , hgvsp ):
## print "biomine::variant::mafvariant::splitHGVSp - "
hgvsp = unquote(hgvsp)
ref = ""
pos = ""
mut = ""
Expand All @@ -278,7 +280,7 @@ def splitHGVSp( self , hgvsp ):
#TODO handle splice variants: NM_000030.2:c.424-2A>G NP_000021.1:p.Gly_142Gln145del
changep = re.match( "p\.([a-zA-Z\*]+?)([0-9\?]+?)([a-zA-Z]{1,3}|[\*\?])(ext[0-9\*\?]*)*" , hgvsp )
changee = re.match( "(e)([0-9]+?)([\+\-][0-9]+?)" , hgvsp )
unknown = re.match( "p\.[\?\=\|(\=\)|0|0\?]" , hgvsp )
unknown = re.match( "p\..*[\?\=\|(\=\)|0|0\?]" , hgvsp )
if changep: #peptide
ref = changep.group( 1 )
pos = changep.group( 2 )
Expand Down