Merge remote-tracking branch 'origin/hotfix'

docs/conf.py

@@ -69,7 +69,7 @@
 # The short X.Y version.
 version = '3.0'
 # The full version, including alpha/beta/rc tags.
-release = '3.0.1'
+release = '3.0.2'
 
 
 # The language for content autogenerated by Sphinx. Refer to documentation

docs/index.rst

@@ -56,22 +56,9 @@ New in Release |release|
 
 This is a bugfix release. It fixes the following problem(s):
 
-- There was small issue in pVACview where picking a different number of
-  variants in the main table would cause changes to variant evaluations
-  to not be recorded correctly.
-- This release also fixes a problem where loading a new set of files into
-  pVACview would not reset previous evaluation summary counts.
-- This release fixes an error in pVACtools that would occur when a chromosomal
-  region in the somatic VCF is not present in the proximal VCF.
-- This release adds further error checking for malformed CSQ header
-  descriptions.
-- This release updates various code portions to remove deprecation warnings and
-  add support for  newer versions of certain dependencies (e.g. pandas).
-- This release fixes an bug with the standalone ``pvacseq
-  calculate_reference_proteome_similarity`` command where picking a custom
-  ``--match-length`` would throw an error.
-- Some users were reporting errors during the tmp file cleanup stages of
-  running the various pipelines. This releases fixes that issue.
+- Newer versions of Ensembl annotations added genes without a HUGO gene name.
+  Variants on those genes cause downstream errors in the aggregate report creation when running
+  the pVACseq pipeline. This release fixes this error.
 
 
 New in Version |version|

docs/releases/3_0.rst

@@ -90,3 +90,12 @@ This is a bugfix release. It fixes the following problem(s):
   ``--match-length`` would throw an error.
 - Some users were reporting errors during the tmp file cleanup stages of
   running the various pipelines. This releases fixes that issue.
+
+Version 3.0.2
+-------------
+
+This is a bugfix release. It fixes the following problem(s):
+
+- Newer versions of Ensembl annotations added genes without a HUGO gene name.
+  Variants on those genes cause downstream errors in the aggregate report creation when running
+  the pVACseq pipeline. This release fixes this error.

pvactools/lib/input_file_converter.py

@@ -331,6 +331,8 @@ def execute(self):
                         else:
                             amino_acid_change_position = protein_position + transcript['Amino_acids']
                     gene_name = transcript['SYMBOL']
+                    if gene_name is None or gene_name == '':
+                        gene_name = transcript['Gene']
                     index = pvactools.lib.run_utils.construct_index(count, gene_name, transcript_name, consequence, amino_acid_change_position)
                     if index in indexes:
                         sys.exit("Warning: TSV index already exists: {}".format(index))

setup.py

@@ -44,7 +44,7 @@
 
 setup(
     name="pvactools",
-    version="3.0.1",
+    version="3.0.2",
     packages=[
         "pvactools.tools",
         "pvactools.tools.pvacbind",

tests/test_data/input_file_converter/output_no_gene_name.tsv

@@ -0,0 +1,2 @@
+chromosome_name	start	stop	reference	variant	gene_name	transcript_name	transcript_support_level	amino_acid_change	codon_change	ensembl_gene_id	hgvsc	hgvsp	wildtype_amino_acid_sequence	frameshift_amino_acid_sequence	fusion_amino_acid_sequence	variant_type	protein_position	transcript_expression	gene_expression	normal_depth	normal_vaf	tdna_depth	tdna_vaf	trna_depth	trna_vaf	index	protein_length_change
+chr22	19718758	19718759	C	A	ENSG00000284874	ENST00000455843.5	1	Q/K	Cag/Aag	ENSG00000284874	ENST00000455843.5:c.22C>A	ENSP00000391731.1:p.Gln8Lys	MDSLAAPQDRLVEQLLSPRTQAQRRLKDIDKQYVGFATLPNQVHRKSVKKGFDFTLMVAGESGLGKSTLVHSLFLTDLYKDRKLLSAEERISQTVEILKHTVDIEEKGVKLKLTIVDTPGFGDAVNNTECWKPITDYVDQQFEQYFRDESGLNRKNIQDNRVHCCLYFISPFGHGLRPVDVGFMKALHEKVNIVPLIAKADCLVPSEIRKLKERIREEIDKFGIHVYQFPECDSDEDEDFKQQDRELKESAPFAVIGSNTVVEAKGQRVRGRLYPWGIVEVENQAHCDFVKLRNMLIRTHMHDLKDVTCDVHYENYRAHCIQQMTSKLTQDSRMESPIPILPLPTPDAETEKLIRMKDEELRRMQEMLQRMKQQMQDQ			missense	8	NA	24.270958	NA	NA	0	0.0	12	0.0	1.ENSG00000284874.ENST00000455843.5.missense.8Q/K	

tests/test_input_file_converter.py

@@ -495,3 +495,18 @@ def test_protein_altering_variants(self):
         self.assertFalse(converter.execute())
         expected_output_file = os.path.join(self.test_data_dir, 'output_protein_altering_variants.tsv')
         self.assertTrue(cmp(convert_vcf_output_file.name, expected_output_file))
+
+    def test_no_gene_name(self):
+        convert_vcf_input_file  = os.path.join(self.test_data_dir, 'input_no_gene_name.vcf')
+        convert_vcf_output_file = tempfile.NamedTemporaryFile()
+
+        convert_vcf_params = {
+            'input_file'        : convert_vcf_input_file,
+            'output_file'       : convert_vcf_output_file.name,
+            'sample_name'       : 'TUMOR',
+        }
+        converter = VcfConverter(**convert_vcf_params)
+
+        self.assertFalse(converter.execute())
+        expected_output_file = os.path.join(self.test_data_dir, 'output_no_gene_name.tsv')
+        self.assertTrue(cmp(convert_vcf_output_file.name, expected_output_file))