From 8780a9097c404afe4d4729301129b1f80010240d Mon Sep 17 00:00:00 2001 From: Maryam Date: Thu, 27 Aug 2026 10:28:39 -0700 Subject: [PATCH 1/3] do not output a df if empty --- bygul/_cli.py | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/bygul/_cli.py b/bygul/_cli.py index 8e40e08..c716f4f 100644 --- a/bygul/_cli.py +++ b/bygul/_cli.py @@ -362,9 +362,8 @@ 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__": From 2c75af1328a0a157d981d06de57c7017e74f5c91 Mon Sep 17 00:00:00 2001 From: Maryam Date: Thu, 27 Aug 2026 10:34:01 -0700 Subject: [PATCH 2/3] make reference optional for primer check function --- bygul/_cli.py | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/bygul/_cli.py b/bygul/_cli.py index c716f4f..b1aed1f 100644 --- a/bygul/_cli.py +++ b/bygul/_cli.py @@ -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, @@ -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] From 9d2b2992f86c64bbf310d299f8f3ca2fbea398eb Mon Sep 17 00:00:00 2001 From: Maryam Date: Thu, 27 Aug 2026 10:34:20 -0700 Subject: [PATCH 3/3] update the test according to the change --- bygul/tests/data/test_cli.py | 1 - 1 file changed, 1 deletion(-) diff --git a/bygul/tests/data/test_cli.py b/bygul/tests/data/test_cli.py index 5341ce2..a0be237 100644 --- a/bygul/tests/data/test_cli.py +++ b/bygul/tests/data/test_cli.py @@ -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"))