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src/jflow/featureio.py

@@ -20,7 +20,7 @@ import os
 from jflow.xopen import xopen
 from jflow.seqio import FormatError
 from jflow.seqio import UnknownFileType
-
+import re
 
 def boolify(s):
     return {'True': True, 'False': False}[s]
@@ -94,7 +94,9 @@ class GFF3Reader(_AbstractFeatureReader):
         if len(row) != 9 : raise FormatError('Invalid number of columns in your GFF3 file {0}'.format( len(row)))
         attributes = {}
         if row[8] and row[8] != '.' :
-            attributes = { p.split('=')[0] : p.split('=')[1]  for p in row[8].split(';')}
+            for p in row[8].split(';') :
+                if p != ""  :
+                    attributes[p.split('=')[0]] = p.split('=')[1]
         
         return Entry(**{'seqid' : row[0], 'source' : row[1], 'type' : row[2], 'start' : int(row[3]), 'end' : int(row[4]),
                       'score' : row[5], 'strand' : row[6], 'phase' : row[7], 'attributes' : attributes  })
@@ -251,12 +253,12 @@ class VCFReader(_AbstractFeatureReader):
         
         if row[7] != '.' :
             variation.addattr( 'info', { p.split('=')[0] : autocast(p.split('=')[1])  for p in row[7].split(';') })
-        
+        regexp_none=re.compile("\.(\/\.)*")
         format = row[8].split(':')
         for lib_infos in range (9,len(row)) :
-            if row[lib_infos] not in [ '.', './.'] :
+            if not regexp_none.match(row[lib_infos]):
                 sformat = row[lib_infos].split(':')
-                variation.samples.append( Entry(**{ autocast(format[i]) : autocast(sformat[i]) for i in range(0,len(format)) }) )
+                variation.samples.append( Entry(**{ autocast(format[i]) : autocast(sformat[i]) if sformat[i] != '.' else None for i in range(0,len(format)) } )  )
             else :
                 variation.samples.append( Entry(**{ autocast(format[i]) : None for i in range(0,len(format)) }) )
         return variation