Merge pull request #332 from susannasiebert/frameshift_error

Fix bug with handling certain frameshift variants
griffithlab · Aug 30, 2017 · 57574f0 · 57574f0
2 parents 6480a00 + ad930b0
commit 57574f0
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Showing 5 changed files with 33 additions and 1 deletion.
diff --git a/pvacseq/lib/generate_fasta.py b/pvacseq/lib/generate_fasta.py
@@ -93,7 +93,10 @@ def main(args_input = sys.argv[1:]):
         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 == '-':

diff --git a/tests/test_data/generate_fasta/input_frameshift_variant_position_shift.tsv b/tests/test_data/generate_fasta/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
diff --git a/tests/test_data/generate_fasta/output_frameshift_variant_position_shift.fasta b/tests/test_data/generate_fasta/output_frameshift_variant_position_shift.fasta
@@ -0,0 +1,4 @@
+>1
+GEIAKSYAELIKQMWSGKFS
+>2
+GEIAKSYAELYQANVVWKV
diff --git a/tests/test_data/generate_fasta/output_frameshift_variant_position_shift.key b/tests/test_data/generate_fasta/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
diff --git a/tests/test_generate_fasta.py b/tests/test_generate_fasta.py
@@ -365,6 +365,25 @@ 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()
+
+        self.assertFalse(call([
+            self.python,
+            self.executable,
+            generate_fasta_input_file,
+            self.peptide_sequence_length,
+            self.epitope_length,
+            generate_fasta_output_file.name,
+            generate_fasta_key_output_file.name,
+        ], shell=False))
+        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()