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Fix AA string #29

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Merged
nbtm-sh merged 1 commit into from
Apr 14, 2025
Merged

Fix AA string #29

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22 changes: 11 additions & 11 deletions samplesheetutils/binaries/create_samplesheet.py
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Original file line number Diff line number Diff line change
Expand Up @@ -139,11 +139,11 @@ def create_samplesheet():

samplesheet_path = args.output_file

for file_name in file_list:
with open(file_name, "r") as fp:
for i_file_name in file_list:
with open(i_file_name, "r") as fp:
fasta_data = read_fasta(fp, read_data=True, single_line=(not args.monomer))
sample_data.extend(fasta_data)
logger.debug(f"Added sample {file_name}, {fasta_data}")
logger.debug(f"Added sample {i_file_name}, {fasta_data}")

samplesheet_path = args.output_file
logger.debug(f"Sample data array length: {len(sample_data)}")
Expand All @@ -154,8 +154,8 @@ def create_samplesheet():
file_list = [os.path.join(args.dir, f) for f in os.listdir(args.dir) if os.path.isfile(os.path.join(args.dir, f)) and re.search(args.fasta_regex, f)]
sample_data = []

for file_name in file_list:
with open(file_name, "r") as file_fp:
for i_file_name in file_list:
with open(i_file_name, "r") as file_fp:
sample_data.extend(read_fasta(file_fp, read_data=True, single_line=False))

samplesheet_path = args.output_file
Expand All @@ -168,21 +168,21 @@ def create_samplesheet():
logger.debug(f"File list aginst regex: {file_list}")
sample_data = []

for file_name in file_list:
with open(file_name, "r") as fp:
for i_file_name in file_list:
with open(i_file_name, "r") as fp:
fasta_data = read_fasta(fp, read_data=True, single_line=False)
# Attempt to find MSA if the MSA directory flag is set
if args.msa_dir:
logger.debug(f"Searching for MSAs of {file_name}")
logger.debug(f"Searching for MSAs of {i_file_name}")
for fsi, i in zip(fasta_data, range(len(fasta_data))):
logger.debug("Checking for " + os.path.join(args.msa_dir, f"{fsi.name}.m3a"))
if os.path.isfile(os.path.join(args.msa_dir, f"{fsi.name}.m3a")):
fasta_data[i].msa = os.path.join(args.msa_dir, f"{fsi.name}.m3a")
logger.debug(f"Added pre-computed MSA for sample {fsi.name} of {file_name}: {fsi.msa}")
logger.debug(f"Added pre-computed MSA for sample {fsi.name} of {i_file_name}: {fsi.msa}")
else:
logger.debug(f"Corresponding MSA for sample {fsi.name} of {file_name} was not found, despite --msa-dir being set. Expected file name is {fsi.name}.m3a. Continuing with no MSA...")
logger.debug(f"Corresponding MSA for sample {fsi.name} of {i_file_name} was not found, despite --msa-dir being set. Expected file name is {fsi.name}.m3a. Continuing with no MSA...")
sample_data.extend(fasta_data)
logger.debug(f"Added sample {file_name}, {fasta_data}")
logger.debug(f"Added sample {i_file_name}, {fasta_data}")
logger.debug(f"Sample data {sample_data[-1].data}")

if args.output_file == "samplesheet.csv":
Expand Down