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fix strip #44

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Merged
nbtm-sh merged 2 commits into from
Jul 24, 2025
Merged

fix strip #44

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27344d7
fix strip
nbtm-sh Jul 24, 2025
31bf60e
update version
nbtm-sh Jul 24, 2025
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18 changes: 9 additions & 9 deletions samplesheetutils/binaries/create_samplesheet.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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():
Expand Down Expand Up @@ -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
Expand All @@ -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":
Expand All @@ -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":
Expand Down Expand Up @@ -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)

Expand Down
2 changes: 1 addition & 1 deletion samplesheetutils/binaries/truncate_msa.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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():
Expand Down
2 changes: 1 addition & 1 deletion setup.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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(),
Expand Down