diff --git a/biomine/variant/mafvariant.py b/biomine/variant/mafvariant.py index 6b03d97..8316f80 100644 --- a/biomine/variant/mafvariant.py +++ b/biomine/variant/mafvariant.py @@ -1,5 +1,6 @@ import re from biomine.variant.variant import variant +from urllib2 import unquote class mafvariant(variant): nonCoding = re.compile( "([NULL|\*|\+|\-])" ) @@ -260,6 +261,7 @@ def HGVSp( self ): return hgvsp def splitHGVSp( self , hgvsp ): ## print "biomine::variant::mafvariant::splitHGVSp - " + hgvsp = unquote(hgvsp) ref = "" pos = "" mut = "" @@ -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 )