Merge branch 'hotfix' of github.com:griffithlab/pVAC-Seq into develop

pvacseq/lib/binding_filter.py

@@ -56,7 +56,6 @@ def main(args_input = sys.argv[1:]):
     writer.writeheader()
 
     for entry in reader:
-        name = entry['Gene Name']
         if args.top_score_metric == 'median':
             score = float(entry['Median MT Score'])
             fold_change = sys.maxsize if entry['Median Fold Change'] == 'NA' else float(entry['Median Fold Change'])

pvacseq/lib/fasta_generator.py

@@ -94,7 +94,10 @@ def execute(self):
             variant_type = line['variant_type']
             full_wildtype_sequence = line['wildtype_amino_acid_sequence']
             if variant_type == 'FS':
-                position = int(line['protein_position'].split('-', 1)[0]) - 1
+                if line['amino_acid_change'] is not None and line['amino_acid_change'].split('/')[0] == '-':
+                    position = int(line['protein_position'].split('-', 1)[0])
+                else:
+                    position = int(line['protein_position'].split('-', 1)[0]) - 1
             elif variant_type == 'missense' or variant_type == 'inframe_ins':
                 wildtype_amino_acid, mutant_amino_acid = line['amino_acid_change'].split('/')
                 if wildtype_amino_acid == '-':
@@ -130,6 +133,8 @@ def execute(self):
             else:
                 mutation_start_position, wildtype_subsequence = self.get_wildtype_subsequence(position, full_wildtype_sequence, wildtype_amino_acid_length, peptide_sequence_length, line)
                 mutation_end_position = mutation_start_position + wildtype_amino_acid_length
+                if wildtype_amino_acid != '-' and wildtype_amino_acid != wildtype_subsequence[mutation_start_position:mutation_end_position]:
+                    sys.exit("ERROR: There was a mismatch between the actual wildtype amino acid and the expected amino acid. Did you use the same reference build version for VEP that you used for creating the VCF?\n%s" % line)
                 mutant_subsequence = wildtype_subsequence[:mutation_start_position] + mutant_amino_acid + wildtype_subsequence[mutation_end_position:]
 
             if '*' in wildtype_subsequence or '*' in mutant_subsequence:

tests/test_data/fasta_generator/input_frameshift_variant_position_shift.tsv

@@ -0,0 +1,2 @@
+chromosome_name	start	stop	reference	variant	gene_name	transcript_name	amino_acid_change	ensembl_gene_id	wildtype_amino_acid_sequence	downstream_amino_acid_sequence	variant_type	protein_position	transcript_expression	gene_expression	normal_depth	normal_vaf	tdna_depth	tdna_vaf	trna_depth	trna_vaf	index
+12	62381609	62381609	G	GT	USP15	ENST00000280377	-/X	ENSG00000135655	MAEGGAADLDTQRSDIATLLKTSLRKGDTWYLVDSRWFKQWKKYVGFDSWDKYQMGDQNVYPGPIDNSGLLKDGDAQSLKEHLIDELDYILLPTEGWNKLVSWYTLMEGQEPIARKVVEQGMFVKHCKVEVYLTELKLCENGNMNNVVTRRFSKADTIDTIEKEIRKIFSIPDEKETRLWNKYMSNTFEPLNKPDSTIQDAGLYQGQVLVIEQKNEDGTWPRGPSTPKSPGASNFSTLPKISPSSLSNNYNNMNNRNVKNSNYCLPSYTAYKNYDYSEPGRNNEQPGLCGLSNLGNTCFMNSAIQCLSNTPPLTEYFLNDKYQEELNFDNPLGMRGEIAKSYAELIKQMWSGKFSYVTPRAFKTQVGRFAPQFSGYQQQDCQELLAFLLDGLHEDLNRIRKKPYIQLKDADGRPDKVVAEEAWENHLKRNDSIIVDIFHGLFKSTLVCPECAKISVTFDPFCYLTLPLPMKKERTLEVYLVRMDPLTKPMQYKVVVPKIGNILDLCTALSALSGIPADKMIVTDIYNHRFHRIFAMDENLSSIMERDDIYVFEININRTEDTEHVIIPVCLREKFRHSSYTHHTGSSLFGQPFLMAVPRNNTEDKLYNLLLLRMCRYVKISTETEETEGSLHCCKDQNINGNGPNGIHEEGSPSEMETDEPDDESSQDQELPSENENSQSEDSVGGDNDSENGLCTEDTCKGQLTGHKKRLFTFQFNNLGNTDINYIKDDTRHIRFDDRQLRLDERSFLALDWDPDLKKRYFDENAAEDFEKHESVEYKPPKKPFVKLKDCIELFTTKEKLGAEDPWYCPNCKEHQQATKKLDLWSLPPVLVVHLKRFSYSRYMRDKLDTLVDFPINDLDMSEFLINPNAGPCRYNLIAVSNHYGGMGGGHYTAFAKNKDDGKWYYFDDSSVSTASEDQIVSKAAYVLFYQRQDTFSGTGFFPLDRETKGASAATGIPLESDEDSNDNDNDIENENCMHTN	YQANVVWKV	FS	345-346	NA	NA	NA	NA	NA	NA	NA	NA	USP15_ENST00000280377_1.FS.345-346

tests/test_data/fasta_generator/output_frameshift_variant_position_shift.fasta

@@ -0,0 +1,4 @@
+>1
+GEIAKSYAELIKQMWSGKFS
+>2
+GEIAKSYAELYQANVVWKV

tests/test_data/fasta_generator/output_frameshift_variant_position_shift.key

@@ -0,0 +1,4 @@
+1:
+- WT.USP15_ENST00000280377_1.FS.345-346
+2:
+- MT.USP15_ENST00000280377_1.FS.345-346

tests/test_fasta_generator.py

@@ -398,6 +398,27 @@ def test_input_file_with_frameshift_variant_range_generates_expected_file(self):
         expected_key_output_file = os.path.join(self.test_data_dir, 'output_frameshift_variant_range.key')
         self.assertTrue(cmp(generate_fasta_key_output_file.name, expected_key_output_file))
 
+    def test_input_file_with_frameshift_variant_position_shift_generates_expected_file(self):
+        generate_fasta_input_file      = os.path.join(self.test_data_dir, 'input_frameshift_variant_position_shift.tsv')
+        generate_fasta_output_file     = tempfile.NamedTemporaryFile()
+        generate_fasta_key_output_file = tempfile.NamedTemporaryFile()
+
+        generate_fasta_params = {
+            'input_file': generate_fasta_input_file,
+            'peptide_sequence_length': self.peptide_sequence_length,
+            'epitope_length': self.epitope_length,
+            'output_file': generate_fasta_output_file.name,
+            'output_key_file': generate_fasta_key_output_file.name,
+            'downstream_sequence_length': None,
+        }
+        generator = FastaGenerator(**generate_fasta_params)
+
+        self.assertFalse(generator.execute())
+        expected_output_file = os.path.join(self.test_data_dir, 'output_frameshift_variant_position_shift.fasta')
+        self.assertTrue(cmp(generate_fasta_output_file.name, expected_output_file))
+        expected_key_output_file = os.path.join(self.test_data_dir, 'output_frameshift_variant_position_shift.key')
+        self.assertTrue(cmp(generate_fasta_key_output_file.name, expected_key_output_file))
+
     def test_input_file_with_sequence_containing_asterisk(self):
         generate_fasta_input_file      = os.path.join(self.test_data_dir, 'input_asterisk_sequence.tsv')
         generate_fasta_output_file     = tempfile.NamedTemporaryFile()