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primer check - do not output empty df, make reference optional address #40 #41 #46

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Merged
mariaelf97 merged 3 commits into from
Aug 27, 2026
Merged

primer check - do not output empty df, make reference optional address #40 #41 #46

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8780a90
do not output a df if empty
mariaelf97 Aug 27, 2026
2c75af1
make reference optional for primer check function
mariaelf97 Aug 27, 2026
9d2b299
update the test according to the change
mariaelf97 Aug 27, 2026
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15 changes: 10 additions & 5 deletions bygul/_cli.py
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Original file line number Diff line number Diff line change
Expand Up @@ -293,7 +293,12 @@ def simulate_proportions(
@click.argument(
"primers", type=str
)
@click.argument("reference", type=str)
@click.option(
"--reference",
default="NA",
type=str,
help="Reference sequence file"
)
@click.option(
"--maxmismatch",
default=1,
Expand All @@ -315,7 +320,8 @@ def check_primers(genomes, primers,
process_primer_check_worker,
)
# read the reference sequence
reference = next(SeqIO.parse(reference, "fasta"))
if reference != "NA":
reference = next(SeqIO.parse(reference, "fasta"))
genome_map = defaultdict(list)
for record in SeqIO.parse(genomes, "fasta"):
sample = record.id.split("_")[0]
Expand Down Expand Up @@ -362,9 +368,8 @@ def check_primers(genomes, primers,
# Concatenate all successful DataFrames
if dfs:
final_df = pd.concat(dfs, ignore_index=True)
else:
final_df = pd.DataFrame()
final_df.to_csv(os.path.join(outdir, "amplicon_stats.csv"), index=False)
final_df.to_csv(os.path.join(outdir,
"amplicon_stats.csv"), index=False)


if __name__ == "__main__":
Expand Down
1 change: 0 additions & 1 deletion bygul/tests/data/test_cli.py
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Expand Up @@ -129,7 +129,6 @@ def test_check_primers(self):
"bygul check-primers "
"bygul/tests/data/ATM-2FFMD73N3.fasta "
"bygul/tests/data/ARTIC_V4-1.bed "
"bygul/tests/data/reference.fasta"
)
self.assertTrue(file_exists(".", "amplicon_stats.csv"))

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