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feat: Warn if samples are missing in FASTA #17

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Merged
gp201 merged 5 commits into from
Mar 10, 2026
Merged

feat: Warn if samples are missing in FASTA #17

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99b6386
Warn if many samples missing in FASTA
gp201 Mar 10, 2026
99eaa53
lint: fix lint for test_ref_muts.py
gp201 Mar 10, 2026
a94bc99
update comment
gp201 Mar 10, 2026
5a26b63
Warn about missing samples and remove ValueError
gp201 Mar 10, 2026
7285193
lint: lint fix
gp201 Mar 10, 2026
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22 changes: 13 additions & 9 deletions barcodeforge/ref_muts.py
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Original file line number Diff line number Diff line change
Expand Up @@ -133,6 +133,14 @@ def process_and_reroot_lineages(
seqs = SeqIO.to_dict(SeqIO.parse(sequences_fasta_path, "fasta"))
ref = SeqIO.read(reference_fasta_path, "fasta")

sample_ids = set(sample_muts_df["sample"])
missing_count = len(sample_ids - set(seqs.keys()))
if missing_count:
total_count = len(sample_ids)
console.print(
f"[{STYLES['warning']}]Warning: {missing_count} out of {total_count} samples ({missing_count / total_count:.1%}) were not found in the FASTA file.[/{STYLES['warning']}]"
)

# if reference in the sample mutations file, use that as the root
if sample_muts_df[sample_muts_df["sample"] == ref.id].shape[0] > 0:
console.print(
Expand Down Expand Up @@ -170,18 +178,14 @@ def process_and_reroot_lineages(
)
seq = seqs.get(sample_id, None)
if seq is None:
# It's better to raise an error or handle this case explicitly
console.print(
f"[{STYLES['warning']}]Warning: Sample {sample_id} not found in FASTA file. Skipping.[/{STYLES['warning']}]"
)
# In debug mode, log a per-sample warning and track missing samples for a summary warning below.
if debug:
console.print(
f"[{STYLES['warning']}]Warning: Sample {sample_id} not found in FASTA file. Skipping.[/{STYLES['warning']}]"
)
continue
root_seqs.append(_construct_root_sequence(root_muts, seq))

if not root_seqs:
raise ValueError(
"No valid root sequences could be generated. Check input FASTA and sample mutations."
)

root = _derive_root_sequence(root_seqs)
additional_muts = _compare_sequences(ref, root)

Expand Down
148 changes: 103 additions & 45 deletions tests/test_ref_muts.py
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Original file line number Diff line number Diff line change
Expand Up @@ -320,54 +320,14 @@ def test_process_and_reroot_lineages_ref_not_in_muts_infer_root(
pd.testing.assert_frame_equal(original_lineages_df, rerooted_lineages_df)


def test_process_and_reroot_lineages_value_error_empty_root_seqs(
sample_ref_fasta_file,
sample_lineage_paths_file,
tmp_path,
mocker,
):
# sample_muts_df is not empty, but no corresponding sequences are found.
muts_content = (
"sampleD\tgene1:A1T\nsampleE\tgene1:C2G" # These samples are not in seqs_file
)
muts_file = tmp_path / "empty_root_seqs_muts.tsv"
muts_file.write_text(muts_content)

# Empty sequences.fasta or sequences that don't match sampleD/sampleE
seqs_content = ">sampleA\nATGC\n>sampleB\nCGTA"
seqs_file = tmp_path / "empty_root_seqs_sequences.fasta"
seqs_file.write_text(seqs_content)

output_additional_muts = tmp_path / "additional_muts_value_error.tsv"
output_rerooted_lineages = tmp_path / "rerooted_lineages_value_error.tsv"

mocked_console = MagicMock(
spec=Console
) # Though not strictly needed for ValueError, good for consistency
mocker.patch("barcodeforge.ref_muts.console", mocked_console)

with pytest.raises(
ValueError,
match="No valid root sequences could be generated. Check input FASTA and sample mutations.",
):
process_and_reroot_lineages(
debug=False,
sample_muts_path=str(muts_file),
reference_fasta_path=sample_ref_fasta_file,
sequences_fasta_path=str(seqs_file),
input_lineage_paths_path=sample_lineage_paths_file,
output_additional_muts_path=str(output_additional_muts),
output_rerooted_lineage_paths_path=str(output_rerooted_lineages),
)


def test_process_and_reroot_lineages_warning_missing_sample_in_fasta(
sample_ref_fasta_file, # ref_genome
sample_lineage_paths_file,
tmp_path,
mocker,
):
# sample_muts_path with sampleA (valid) and sampleMissing (not in FASTA)
# 1 out of 2 samples missing, so summary warning is printed
muts_content = "sampleA\tgene1:A2T,A7G\nsampleMissing\tgene1:C1G"
muts_file = tmp_path / "missing_fasta_sample_muts.tsv"
muts_file.write_text(muts_content)
Expand Down Expand Up @@ -400,15 +360,22 @@ def test_process_and_reroot_lineages_warning_missing_sample_in_fasta(
assert output_additional_muts.exists()
assert output_rerooted_lineages.exists()

# Verify warning for missing sample
expected_warning_call_substr = (
"[yellow]Warning: Sample sampleMissing not found in FASTA file. Skipping."
)
# Verify summary warning is shown (any missing samples triggers warning)
expected_warning_call_substr = "1 out of 2 samples"
assert any(
expected_warning_call_substr in str(c_args)
for c_args in mocked_console.print.call_args_list
)

# Verify per-sample warning is NOT shown when debug=False
per_sample_warning_substr = (
"Sample sampleMissing not found in FASTA file. Skipping."
)
assert not any(
per_sample_warning_substr in str(c_args)
for c_args in mocked_console.print.call_args_list
)

# Verify inference based on sampleA
df_add_muts = pd.read_csv(output_additional_muts, sep="\t")
assert "position" in df_add_muts.columns or df_add_muts.empty
Expand All @@ -424,3 +391,94 @@ def test_process_and_reroot_lineages_warning_missing_sample_in_fasta(
)
else:
pd.testing.assert_frame_equal(original_lineages_df, rerooted_lineages_df)


def test_process_and_reroot_lineages_debug_shows_per_sample_warning(
sample_ref_fasta_file, # ref_genome
sample_lineage_paths_file,
tmp_path,
mocker,
):
# When debug=True, the per-sample warning should be shown for each missing sample
muts_content = "sampleA\tgene1:A2T,A7G\nsampleMissing\tgene1:C1G"
muts_file = tmp_path / "debug_missing_muts.tsv"
muts_file.write_text(muts_content)

seqs_content = ">sampleA\nATAAAAAGAA\n>sampleOther\nCCCCCCCCCC"
seqs_file = tmp_path / "debug_missing_seqs.fasta"
seqs_file.write_text(seqs_content)

output_additional_muts = tmp_path / "additional_muts_debug.tsv"
output_rerooted_lineages = tmp_path / "rerooted_lineages_debug.tsv"

mocked_console = MagicMock(spec=Console)
mocker.patch("barcodeforge.ref_muts.console", mocked_console)

process_and_reroot_lineages(
debug=True,
sample_muts_path=str(muts_file),
reference_fasta_path=sample_ref_fasta_file,
sequences_fasta_path=str(seqs_file),
input_lineage_paths_path=sample_lineage_paths_file,
output_additional_muts_path=str(output_additional_muts),
output_rerooted_lineage_paths_path=str(output_rerooted_lineages),
)

# Verify per-sample warning IS shown when debug=True
per_sample_warning_substr = (
"Sample sampleMissing not found in FASTA file. Skipping."
)
assert any(
per_sample_warning_substr in str(c_args)
for c_args in mocked_console.print.call_args_list
)


def test_process_and_reroot_lineages_summary_warning_any_missing(
sample_ref_fasta_file,
sample_lineage_paths_file,
tmp_path,
mocker,
):
# 1 out of 5 samples missing — warning is always shown when any samples are missing
muts_content = (
"sampleA\tgene1:A2T\n"
"sampleB\tgene1:A6G\n"
"sampleC\tgene1:A3T\n"
"sampleD\tgene1:A4T\n"
"sampleMissing\tgene1:C1G"
)
muts_file = tmp_path / "below_threshold_muts.tsv"
muts_file.write_text(muts_content)

seqs_content = (
">sampleA\nATAAAAAGAA\n"
">sampleB\nAAAAAAGAAA\n"
">sampleC\nAAATAAAAAA\n"
">sampleD\nAAAATAAAAA\n"
)
seqs_file = tmp_path / "below_threshold_seqs.fasta"
seqs_file.write_text(seqs_content)

output_additional_muts = tmp_path / "additional_muts_below.tsv"
output_rerooted_lineages = tmp_path / "rerooted_lineages_below.tsv"

mocked_console = MagicMock(spec=Console)
mocker.patch("barcodeforge.ref_muts.console", mocked_console)

process_and_reroot_lineages(
debug=False,
sample_muts_path=str(muts_file),
reference_fasta_path=sample_ref_fasta_file,
sequences_fasta_path=str(seqs_file),
input_lineage_paths_path=sample_lineage_paths_file,
output_additional_muts_path=str(output_additional_muts),
output_rerooted_lineage_paths_path=str(output_rerooted_lineages),
)

# Verify summary warning IS shown even when only 1 out of 5 samples is missing
summary_warning_substr = "were not found in the FASTA file"
assert any(
summary_warning_substr in str(c_args)
for c_args in mocked_console.print.call_args_list
)
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