iskander cr

openvax · Sep 6, 2018 · 43f90cc · 43f90cc
1 parent 86973af
commit 43f90cc
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Showing 4 changed files with 11 additions and 9 deletions.
diff --git a/vaxrank/cli.py b/vaxrank/cli.py
@@ -185,7 +185,8 @@ def add_output_args(arg_parser):
     output_args_group.add_argument(
         "--output-passing-variants-csv",
         default="",
-        help="Path to CSV file containing some metadata about every passing variant")
+        help="Path to CSV file containing some metadata about every variant that has passed all "
+             "variant caller filters")
 
 
 def add_vaccine_peptide_args(arg_parser):

diff --git a/vaxrank/core_logic.py b/vaxrank/core_logic.py
@@ -286,6 +286,9 @@ def variant_properties(self):
         # whether this variant is part of a pathway of interest, is a strong MHC binder, etc.
         variant_properties_dict = OrderedDict()
         for variant in self.variants:
+            gene_name = ''
+            if variant.gene_names:
+                gene_name = variant.effects().top_priority_effect().gene_name
             variant_dict = OrderedDict((
                 ('contig', variant.contig),
                 ('start', variant.start),
@@ -294,7 +297,7 @@ def variant_properties(self):
                 ('is_coding_nonsynonymous', False),
                 ('rna_support', False),
                 ('mhc_binder', False),
-                ('gene_name', variant.gene_names[0] if variant.gene_names else ''),
+                ('gene_name', gene_name),
             ))
             if self.gene_pathway_check is not None:
                 pathway_dict = self.gene_pathway_check.make_variant_dict(variant)

diff --git a/vaxrank/data/class1-mhc-presentation-pathway.csv b/vaxrank/data/class1-mhc-presentation-pathway.csv
@@ -17,4 +17,3 @@ B2M,beta-2 microglobulin,MHC subunit,ENSG00000166710
 HLA-A,human leukocyte antigen A,MHC subunit,ENSG00000206503
 HLA-B,human leukocyte antigen B,MHC subunit,ENSG00000234745
 HLA-C,human leukocyte antigen C,MHC subunit,ENSG00000204525
-
diff --git a/vaxrank/gene_pathway_check.py b/vaxrank/gene_pathway_check.py
@@ -112,15 +112,14 @@ def make_variant_dict(self, variant):
         gene_ids = variant.gene_ids
 
         for gene_id in gene_ids:
-            if any(self.interferon_gamma_response[_ENSEMBL_GENE_ID] == gene_id):
+            if (self.interferon_gamma_response[_ENSEMBL_GENE_ID] == gene_id).any():
                 variant_dict[_IFG_RESPONSE] = True
-            if any(self.class1_mhc_presentation_pathway[_ENSEMBL_GENE_ID] == gene_id):
+            if (self.class1_mhc_presentation_pathway[_ENSEMBL_GENE_ID] == gene_id).any():
                 variant_dict[_CLASS_I_MHC] = True
-            if any(self.cancer_driver_genes[_ENSEMBL_GENE_ID] == gene_id):
+            if (self.cancer_driver_genes[_ENSEMBL_GENE_ID] == gene_id).any():
                 variant_dict[_DRIVER_GENE] = True
-            if len(self.cancer_driver_variants.loc[
-                    (self.cancer_driver_variants[_ENSEMBL_GENE_ID] == gene_id) & 
-                    (self.cancer_driver_variants[_MUTATION] == effect)]) > 0:
+            if ((self.cancer_driver_variants[_ENSEMBL_GENE_ID] == gene_id) &
+                    (self.cancer_driver_variants[_MUTATION] == effect)).any():
                 variant_dict[_DRIVER_VARIANT] = True
 
         return variant_dict