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Sean Davis committed 446365c

Fix issue #2

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  • Parent commits 24831a2

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Files changed (3)

File seqtools/snpeff.py

 
     @property
     def highest(self,impactOrder=impactOrder):
+        """Return the highest impact effect, or None is there is no gene effect"""
         for impact in impactOrder:
             for eff in self.effs:
                 if(eff['Impact'] == impact):

File seqtools/vcf.py

         if(snpeff):
             try:
                 maxeffect = snpEffEffects(record.INFO['EFF']).highest
-                info_row += list(maxeffect.values())
+                if(maxeffect is None):
+                    # effect is as a modifier and chromosome is not found
+                    info_row += ['NA']*len(effNames)
+                else:
+                    info_row += list(maxeffect.values())
             except KeyError:
                 # return a bunch of NAs
                 info_row += ['NA']*len(effNames)
 from setuptools import setup, find_packages
 import sys, os, glob
 
-version = '0.4.5'
+version = '0.4.6'
 
 setup(name='seqtools',
       version=version,