From 27344d7edcb33977fbdfbe5ad6ec4d5bb021a442 Mon Sep 17 00:00:00 2001 From: nbtm-sh Date: Thu, 24 Jul 2025 11:41:23 +1000 Subject: [PATCH 1/2] fix strip --- .../binaries/create_samplesheet.py | 18 +++++++++--------- samplesheetutils/binaries/truncate_msa.py | 2 +- 2 files changed, 10 insertions(+), 10 deletions(-) diff --git a/samplesheetutils/binaries/create_samplesheet.py b/samplesheetutils/binaries/create_samplesheet.py index d679b69..a7676a1 100644 --- a/samplesheetutils/binaries/create_samplesheet.py +++ b/samplesheetutils/binaries/create_samplesheet.py @@ -19,7 +19,7 @@ logging.basicConfig() def version(): - print("samplesheet-utils 1.3.2") + print("samplesheet-utils 1.3.3") #if __name__ == "__main__": def create_samplesheet(): @@ -85,12 +85,12 @@ def create_samplesheet(): if mode == MODE_STRING_CSV: # Generate metadata for AA string - aa_sample_name = sample_name(args.aa_string.strip(), seq_chars=args.seq_chars) + aa_sample_name = sample_name("".join(args.aa_string.strip().split()), seq_chars=args.seq_chars) aa_sample_file_name = file_name(aa_sample_name, prefix=args.aa_prefix, suffix=args.aa_suffix, extension=args.output_extension) aa_path = args.fasta_dir + "/" + aa_sample_file_name # Create the fasta file - sample_data = Sample(aa_sample_name, aa_path, args.aa_string.strip()) + sample_data = Sample(aa_sample_name, aa_path, "".join(args.aa_string.strip().split())) make_fasta(sample_data) # Write the samplesheet @@ -100,12 +100,12 @@ def create_samplesheet(): if mode == MODE_STRING_JSON: # Generate metadata for AA string - aa_sample_name = sample_name(args.aa_string.strip(), seq_chars=args.seq_chars) + aa_sample_name = sample_name("".join(args.aa_string.strip().split()), seq_chars=args.seq_chars) aa_sample_file_name = file_name(aa_sample_name, prefix=args.aa_prefix, suffix=args.aa_suffix, extension=args.output_extension) aa_path = args.fasta_dir + "/" + aa_sample_file_name # Create the fasta file - sample_data = Sample(aa_sample_name, aa_path, args.aa_string.strip()) + sample_data = Sample(aa_sample_name, aa_path, "".join(args.aa_string.strip().split())) make_fasta(sample_data) if args.output_file == "samplesheet.csv": @@ -117,12 +117,12 @@ def create_samplesheet(): if mode == MODE_STRING_YAML: # Generate metadata for AA string - aa_sample_name = sample_name(args.aa_string.strip(), seq_chars=args.seq_chars) + aa_sample_name = sample_name("".join(args.aa_string.strip().split()), seq_chars=args.seq_chars) aa_sample_file_name = file_name(aa_sample_name, prefix=args.aa_prefix, suffix=args.aa_suffix, extension=args.output_extension) aa_path = args.fasta_dir + "/" + aa_sample_file_name # Create the fasta file - sample_data = Sample(aa_sample_name, aa_path, args.aa_string.strip()) + sample_data = Sample(aa_sample_name, aa_path, "".join(args.aa_string.strip().split())) make_fasta(sample_data) if args.output_file == "samplesheet.csv": @@ -198,13 +198,13 @@ def create_samplesheet(): create_yaml_boltz(sample_data, ss_fp) if mode == MODE_STRING_YAML_RFAA: - aa_sample_name = sample_name(args.aa_string, seq_chars=args.seq_chars) + aa_sample_name = sample_name("".join(args.aa_string.strip().split()), seq_chars=args.seq_chars) # overwrite defaults aa_sample_file_name = file_name(aa_sample_name, prefix=args.aa_prefix, suffix=args.aa_suffix, extension="yaml") aa_path = args.fasta_dir + "/" + aa_sample_file_name # Create the fasta file - sample_data = Sample(aa_sample_name, aa_path, args.aa_string) + sample_data = Sample(aa_sample_name, aa_path, "".join(args.aa_string.strip().split())) with open(aa_sample_file_name, "w") as s_fp: create_yaml_rfaa(sample_data, s_fp) diff --git a/samplesheetutils/binaries/truncate_msa.py b/samplesheetutils/binaries/truncate_msa.py index ebfdfa3..055d581 100644 --- a/samplesheetutils/binaries/truncate_msa.py +++ b/samplesheetutils/binaries/truncate_msa.py @@ -11,7 +11,7 @@ logging.basicConfig() def version(): - print("samplesheet-utils 1.3.2") + print("samplesheet-utils 1.3.3") #if __name__ == "__main__": def truncate_msa(): From 31bf60e9e4203c06c9581957d9a8b69064e65fbc Mon Sep 17 00:00:00 2001 From: nbtm-sh Date: Thu, 24 Jul 2025 11:46:46 +1000 Subject: [PATCH 2/2] update version --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 00942a4..a746e0a 100644 --- a/setup.py +++ b/setup.py @@ -2,7 +2,7 @@ setup( name="samplesheetutils", - version="1.3.2", + version="1.3.3", author="nbtm-sh", author_email="n.glades@unsw.edu.au", packages=find_packages(),