From b38f0a123dde257b11020bf1415c25ee264b5cef Mon Sep 17 00:00:00 2001 From: Evelyn Schmidt Date: Tue, 9 Apr 2024 14:07:34 -0500 Subject: [PATCH 1/3] output proximal variants tsv --- pvactools/tools/pvacseq/generate_protein_fasta.py | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/pvactools/tools/pvacseq/generate_protein_fasta.py b/pvactools/tools/pvacseq/generate_protein_fasta.py index 1bab065f..59367b0a 100644 --- a/pvactools/tools/pvacseq/generate_protein_fasta.py +++ b/pvactools/tools/pvacseq/generate_protein_fasta.py @@ -193,6 +193,12 @@ def main(args_input = sys.argv[1:]): temp_dir = tempfile.mkdtemp() proximal_variants_tsv = convert_vcf(args.input_vcf, temp_dir, args.sample_name, args.phased_proximal_variants_vcf, args.flanking_sequence_length, args.pass_only) + if proximal_variants_tsv is not None: + proximal_variants_file = "{}.proximal_variants.tsv".format(args.output_file) + with open(proximal_variants_tsv, 'r') as input_file: + with open(proximal_variants_file, 'w', newline='') as output_file: + output_file.write(input_file.read()) + generate_fasta(args.flanking_sequence_length, downstream_sequence_length, temp_dir, proximal_variants_tsv) parse_files(args.output_file, temp_dir, args.mutant_only, args.input_tsv, args.aggregate_report_evaluation) shutil.rmtree(temp_dir, ignore_errors=True) From 45afab7574f5a1f55d582e985cb2a0f414d4fb8b Mon Sep 17 00:00:00 2001 From: Evelyn Schmidt Date: Tue, 9 Apr 2024 14:44:02 -0500 Subject: [PATCH 2/3] using shutil --- pvactools/tools/pvacseq/generate_protein_fasta.py | 8 ++------ 1 file changed, 2 insertions(+), 6 deletions(-) diff --git a/pvactools/tools/pvacseq/generate_protein_fasta.py b/pvactools/tools/pvacseq/generate_protein_fasta.py index 59367b0a..9c392440 100644 --- a/pvactools/tools/pvacseq/generate_protein_fasta.py +++ b/pvactools/tools/pvacseq/generate_protein_fasta.py @@ -193,12 +193,8 @@ def main(args_input = sys.argv[1:]): temp_dir = tempfile.mkdtemp() proximal_variants_tsv = convert_vcf(args.input_vcf, temp_dir, args.sample_name, args.phased_proximal_variants_vcf, args.flanking_sequence_length, args.pass_only) - if proximal_variants_tsv is not None: - proximal_variants_file = "{}.proximal_variants.tsv".format(args.output_file) - with open(proximal_variants_tsv, 'r') as input_file: - with open(proximal_variants_file, 'w', newline='') as output_file: - output_file.write(input_file.read()) - + proximal_variants_file = "{}.proximal_variants.tsv".format(args.output_file) + shutil.copy(proximal_variants_tsv, proximal_variants_file) generate_fasta(args.flanking_sequence_length, downstream_sequence_length, temp_dir, proximal_variants_tsv) parse_files(args.output_file, temp_dir, args.mutant_only, args.input_tsv, args.aggregate_report_evaluation) shutil.rmtree(temp_dir, ignore_errors=True) From f8ce28d23c81fadf4b32700412aeb6bcd0c298b9 Mon Sep 17 00:00:00 2001 From: Evelyn Schmidt Date: Wed, 10 Apr 2024 09:44:57 -0500 Subject: [PATCH 3/3] adding check before attempting to save proximal variants file --- pvactools/tools/pvacseq/generate_protein_fasta.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/pvactools/tools/pvacseq/generate_protein_fasta.py b/pvactools/tools/pvacseq/generate_protein_fasta.py index 9c392440..a5874702 100644 --- a/pvactools/tools/pvacseq/generate_protein_fasta.py +++ b/pvactools/tools/pvacseq/generate_protein_fasta.py @@ -194,7 +194,8 @@ def main(args_input = sys.argv[1:]): temp_dir = tempfile.mkdtemp() proximal_variants_tsv = convert_vcf(args.input_vcf, temp_dir, args.sample_name, args.phased_proximal_variants_vcf, args.flanking_sequence_length, args.pass_only) proximal_variants_file = "{}.proximal_variants.tsv".format(args.output_file) - shutil.copy(proximal_variants_tsv, proximal_variants_file) + if proximal_variants_tsv is not None: + shutil.copy(proximal_variants_tsv, proximal_variants_file) generate_fasta(args.flanking_sequence_length, downstream_sequence_length, temp_dir, proximal_variants_tsv) parse_files(args.output_file, temp_dir, args.mutant_only, args.input_tsv, args.aggregate_report_evaluation) shutil.rmtree(temp_dir, ignore_errors=True)