Merge pull request #1003 from griffithlab/arriba_invalid_characters

Handle invalid characters in Arriba input files

docs/pvacseq/input_file_prep/proximal_vcf.rst

@@ -110,6 +110,8 @@ ______________________________
 Phase variants using GATK’s ReadBackedPhasing
 _____________________________________________
 
+Unfortunately, the tool used for this step is no longer available in current versions of GATK. We recommend using GATK 3.6.0 to run this step.
+
 .. code-block:: none
 
    /usr/bin/java -Xmx16g -jar /opt/GenomeAnalysisTK.jar \

pvactools/lib/fasta_generator.py

@@ -33,6 +33,13 @@ def __init__(self, **kwargs):
         self.proximal_variants_file     = kwargs.pop('proximal_variants_file', None)
         self.proximal_variants          = self.parse_proximal_variants_file()
 
+
+    def contains_invalid_characters(self, sequence):
+        for character in ['*', 'X', '?']:
+            if character in sequence:
+                return True
+        return False
+
     def position_out_of_bounds(self, position, sequence):
         return position > len(sequence)-1
 
@@ -305,10 +312,7 @@ def execute(self):
             if subsequence.endswith('X'):
                 subsequence = subsequence[:-1]
 
-            if '*' in subsequence:
-                continue
-
-            if 'X' in subsequence:
+            if self.contains_invalid_characters(subsequence):
                 continue
 
             if len(subsequence) < self.epitope_length:

pvactools/tools/pvacfuse/run.py

@@ -211,7 +211,7 @@ def main(args_input = sys.argv[1:]):
             for epitope_length in epitope_lengths:
                 (input_file, per_epitope_output_dir) = generate_fasta(args, output_dir, epitope_length)
                 if os.path.getsize(input_file) == 0:
-                    print("The intermediate FASTA file for epitope length {} is empty. Please check that the input AGfusion directory contains fusion entries with `*_protein.fa` files. Fusion entries without this file cannot be processed by pVACfuse.".format(epitope_length))
+                    print("The intermediate FASTA file for epitope length {} is empty. No processable fusions found.")
                     continue
 
                 run_arguments['input_file']              = input_file

tests/test_data/pvacfuse_generate_protein_fasta/input_with_invalid_character.tsv

@@ -0,0 +1,2 @@
+#gene1	gene2	strand1(gene/fusion)	strand2(gene/fusion)	breakpoint1	breakpoint2	site1	site2	type	split_reads1	split_reads2	discordant_mates	coverage1	coverage2	confidence	reading_frame	tags	retained_protein_domains	closest_genomic_breakpoint1	closest_genomic_breakpoint2	gene_id1	gene_id2	transcript_id1	transcript_id2	direction1	direction2	filters	fusion_transcript	peptide_sequence	read_identifiers
+PTEN	ENSG00000200891(21548),MED6P1(31892)	+/+	./+	chr10:87952259	chr10:88016243	CDS/splice-site	intergenic	deletion/read-through	163	146	6	3691	3002	high	out-of-frame	.	C2_domain_of_PTEN_tumour-suppressor_protein(100%),Dual_specificity_phosphatase__catalytic_domain(100%)|	.	.	ENSG00000171862	.	ENST00000371953	.	downstream	upstream	duplicates(384),low_entropy(4),mismappers(15),mismatches(6),multimappers(2)	CCTCACCTCCATGCAGATGCAGCTGTACCTGCAGCAGCTGCAGAAGGTGCAGCCCCCTACGCCGCTACTCCCTTCCGTGAAGGTGCAGTCCCAGCCCCCcCCCCCCCccCCcCCCCCcCCCCcCCCC|CCC??CCCCC?CCCCCCCTGCCGCCCCCACCCCACCCCTCTGTGCAGCAGCAGCTGCAGCAGCAGCCGCCACCACCCCCACCACCCCAGCCCCAGCCTCCACCCCAGCAGCAGCATCAGCCCCCTCCACGGCCCGTGCACTTGCAGCCCATGCAGTTTTCCACCCA	LTSMQMQLYLQQLQKVQPPTPLLPSVKVQSQPPPPpPPPPpP|p?p?ppcrphptplcssscsssrhhphhpspslhpsssisplhgpctcspcsfpp	K00193:38:H3MYFBBXX:4:1101:18904:31572,K00193:38:H3MYFBBXX:4:1101:20386:3197

tests/test_pvacfuse_generate_protein_fasta.py

@@ -54,3 +54,18 @@ def test_input_tsv(self):
         expected_output_file = os.path.join(self.test_data_dir, 'output_with_tsv.fasta')
         os.unlink("{}.manufacturability.tsv".format(generate_protein_fasta_output_file.name))
         self.assertTrue(cmp(generate_protein_fasta_output_file.name, expected_output_file))
+
+    def test_arriba_tsv_with_invalid_character(self):
+        generate_protein_fasta_input_file  = os.path.join(self.test_data_dir, 'input_with_invalid_character.tsv')
+        generate_protein_fasta_output_file = tempfile.NamedTemporaryFile()
+
+        self.assertFalse(call([
+            self.python,
+            self.executable,
+            generate_protein_fasta_input_file,
+            self.flanking_sequence_length,
+            generate_protein_fasta_output_file.name,
+            '-d', 'full'
+        ], shell=False))
+        os.unlink("{}.manufacturability.tsv".format(generate_protein_fasta_output_file.name))
+        self.assertEqual(os.path.getsize(generate_protein_fasta_output_file.name), 0)