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Fix pseudocigar handling for constructing a PMO #85

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Fix pseudocigar handling for constructing a PMO #85

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99 changes: 98 additions & 1 deletion src/pmotools/pmo_builder/mhap_table_to_pmo.py
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Original file line number Diff line number Diff line change
Expand Up @@ -26,6 +26,13 @@ def mhap_table_to_pmo(
masking_delim: str = ",",
microhaplotype_name_col: str | None = None,
pseudocigar_col: str | None = None,
pseudocigar_chrom_col: str | None = None,
pseudocigar_start_col: str | None = None,
pseudocigar_end_col: str | None = None,
pseudocigar_ref_seq_col: str | None = None,
pseudocigar_strand_col: str | None = None,
pseudocigar_genome_id: int | None = None,
pseudocigar_generation_description_col: str | None = None,
quality_col: str | None = None,
additional_representative_mhap_cols: list | None = None,
additional_mhap_detected_cols: list | None = None,
Expand Down Expand Up @@ -73,6 +80,20 @@ def mhap_table_to_pmo(
:type microhaplotype_name_col: str, optional
:param pseudocigar_col: the name of the column containing a pseudocigar for the microhaplotype
:type pseudocigar_col: str, optional
:param pseudocigar_chrom_col: column for the pseudocigar ref_loc chromosome; defaults to chrom_col
:type pseudocigar_chrom_col: str, optional
:param pseudocigar_start_col: column for the pseudocigar ref_loc start (required if pseudocigar_col is set)
:type pseudocigar_start_col: str, optional
:param pseudocigar_end_col: column for the pseudocigar ref_loc end (required if pseudocigar_col is set)
:type pseudocigar_end_col: str, optional
:param pseudocigar_ref_seq_col: optional column for the pseudocigar ref_loc reference sequence
:type pseudocigar_ref_seq_col: str, optional
:param pseudocigar_strand_col: optional column for the pseudocigar ref_loc strand
:type pseudocigar_strand_col: str, optional
:param pseudocigar_genome_id: genome id for the pseudocigar ref_loc; defaults to genome_id
:type pseudocigar_genome_id: int, optional
:param pseudocigar_generation_description_col: optional column describing how the pseudocigar was generated
:type pseudocigar_generation_description_col: str, optional
:param quality_col: the name of the column containing the ANSI FASTQ per-base quality score for this sequence
:type quality_col: str, optional
:param additional_representative_mhap_cols: additional columns to add to the representative microhaplotypes table
Expand Down Expand Up @@ -100,6 +121,13 @@ def mhap_table_to_pmo(
masking_delim=masking_delim,
microhaplotype_name_col=microhaplotype_name_col,
pseudocigar_col=pseudocigar_col,
pseudocigar_chrom_col=pseudocigar_chrom_col,
pseudocigar_start_col=pseudocigar_start_col,
pseudocigar_end_col=pseudocigar_end_col,
pseudocigar_ref_seq_col=pseudocigar_ref_seq_col,
pseudocigar_strand_col=pseudocigar_strand_col,
pseudocigar_genome_id=pseudocigar_genome_id,
pseudocigar_generation_description_col=pseudocigar_generation_description_col,
quality_col=quality_col,
additional_representative_mhap_cols=additional_representative_mhap_cols,
)
Expand Down Expand Up @@ -160,6 +188,13 @@ def create_representative_microhaplotype_dict(
masking_delim: str = ",",
microhaplotype_name_col: str | None = None,
pseudocigar_col: str | None = None,
pseudocigar_chrom_col: str | None = None,
pseudocigar_start_col: str | None = None,
pseudocigar_end_col: str | None = None,
pseudocigar_ref_seq_col: str | None = None,
pseudocigar_strand_col: str | None = None,
pseudocigar_genome_id: int | None = None,
pseudocigar_generation_description_col: str | None = None,
quality_col: str | None = None,
additional_representative_mhap_cols: list[str] | None = None,
):
Expand Down Expand Up @@ -198,6 +233,20 @@ def create_representative_microhaplotype_dict(
:type microhaplotype_name_col: str, optional
:param pseudocigar_col: the name of the column containing a pseudocigar for the microhaplotype
:type pseudocigar_col: str, optional
:param pseudocigar_chrom_col: column for the pseudocigar ref_loc chromosome; defaults to chrom_col
:type pseudocigar_chrom_col: str, optional
:param pseudocigar_start_col: column for the pseudocigar ref_loc start (required if pseudocigar_col is set)
:type pseudocigar_start_col: str, optional
:param pseudocigar_end_col: column for the pseudocigar ref_loc end (required if pseudocigar_col is set)
:type pseudocigar_end_col: str, optional
:param pseudocigar_ref_seq_col: optional column for the pseudocigar ref_loc reference sequence
:type pseudocigar_ref_seq_col: str, optional
:param pseudocigar_strand_col: optional column for the pseudocigar ref_loc strand
:type pseudocigar_strand_col: str, optional
:param pseudocigar_genome_id: genome id for the pseudocigar ref_loc; defaults to genome_id
:type pseudocigar_genome_id: int, optional
:param pseudocigar_generation_description_col: optional column describing how the pseudocigar was generated
:type pseudocigar_generation_description_col: str, optional
:param quality_col: the name of the column containing the ANSI FASTQ per-base quality score for this sequence
:type quality_col: str, optional
:param additional_representative_mhap_cols: additional columns to add to the representative microhaplotypes table
Expand All @@ -211,6 +260,21 @@ def create_representative_microhaplotype_dict(
microhaplotype_table, additional_representative_mhap_cols
)

# the pseudocigar ref_loc shares the chromosome / genome with the
# microhaplotype location by default, but each may use its own column
ps_chrom_col = pseudocigar_chrom_col if pseudocigar_chrom_col else chrom_col
ps_genome_id = (
pseudocigar_genome_id if pseudocigar_genome_id is not None else genome_id
)
if pseudocigar_col and not (
ps_chrom_col and pseudocigar_start_col and pseudocigar_end_col
):
raise ValueError(
"pseudocigar_col is set, so a Pseudocigar ref_loc must be "
"constructable: set a chromosome (pseudocigar_chrom_col or "
"chrom_col), pseudocigar_start_col, and pseudocigar_end_col."
)

def get_if_present(row, col):
return row[col] if col and pd.notna(row[col]) else None

Expand Down Expand Up @@ -263,6 +327,12 @@ def warn_if_duplicated_seqs(df, target_col, seq_col):
alt_annotations_col,
microhaplotype_name_col,
pseudocigar_col,
ps_chrom_col,
pseudocigar_start_col,
pseudocigar_end_col,
pseudocigar_ref_seq_col,
pseudocigar_strand_col,
pseudocigar_generation_description_col,
quality_col,
]
masking_cols = [
Expand Down Expand Up @@ -319,7 +389,34 @@ def warn_if_duplicated_seqs(df, target_col, seq_col):
if val := get_if_present(row, microhaplotype_name_col):
mhap["microhaplotype_name"] = val
if val := get_if_present(row, pseudocigar_col):
mhap["pseudo_cigar"] = val
if not (
pd.notna(row[ps_chrom_col])
and pd.notna(row[pseudocigar_start_col])
and pd.notna(row[pseudocigar_end_col])
):
raise ValueError(
f"pseudocigar present for target {target}, seq "
f"{row[seq_col]} but its ref_loc chrom/start/end "
"is missing"
)
ref_loc = {
"genome_id": ps_genome_id,
"chrom": row[ps_chrom_col],
"start": row[pseudocigar_start_col],
"end": row[pseudocigar_end_col],
}
if pseudocigar_ref_seq_col and pd.notna(row[pseudocigar_ref_seq_col]):
ref_loc["ref_seq"] = row[pseudocigar_ref_seq_col]
if pseudocigar_strand_col and pd.notna(row[pseudocigar_strand_col]):
ref_loc["strand"] = row[pseudocigar_strand_col]
pseudocigar = {"pseudocigar_seq": val, "ref_loc": ref_loc}
if pseudocigar_generation_description_col and pd.notna(
row[pseudocigar_generation_description_col]
):
pseudocigar["pseudocigar_generation_description"] = row[
pseudocigar_generation_description_col
]
mhap["pseudocigar"] = pseudocigar
if val := get_if_present(row, quality_col):
mhap["quality"] = val
if additional_representative_mhap_cols:
Expand Down
71 changes: 34 additions & 37 deletions tests/test_pmo_builder/test_mhap_table_to_pmo.py
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Original file line number Diff line number Diff line change
Expand Up @@ -510,52 +510,49 @@ def test_create_representative_microhaplotype_dict_with_ad_cols(self):
mhap_table_ad_cols = self.small_mhap_table.copy()
mhap_table_ad_cols["adcol1"] = "this"
mhap_table_ad_cols["adcol2"] = "that"
mhap_table_ad_cols["cig"] = "cigs"

rep_dict_with_ad_cols = copy.deepcopy(self.small_representative_dict)
rep_dict_with_ad_cols["targets"][0]["microhaplotypes"][0]["adcol1"] = "this"
rep_dict_with_ad_cols["targets"][0]["microhaplotypes"][0]["adcol2"] = "that"
rep_dict_with_ad_cols["targets"][0]["microhaplotypes"][0][
"pseudo_cigar"
] = "cigs"
rep_dict_with_ad_cols["targets"][0]["microhaplotypes"][1]["adcol1"] = "this"
rep_dict_with_ad_cols["targets"][0]["microhaplotypes"][1]["adcol2"] = "that"
rep_dict_with_ad_cols["targets"][0]["microhaplotypes"][1][
"pseudo_cigar"
] = "cigs"
rep_dict_with_ad_cols["targets"][0]["microhaplotypes"][2]["adcol1"] = "this"
rep_dict_with_ad_cols["targets"][0]["microhaplotypes"][2]["adcol2"] = "that"
rep_dict_with_ad_cols["targets"][0]["microhaplotypes"][2][
"pseudo_cigar"
] = "cigs"
rep_dict_with_ad_cols["targets"][1]["microhaplotypes"][0]["adcol1"] = "this"
rep_dict_with_ad_cols["targets"][1]["microhaplotypes"][0]["adcol2"] = "that"
rep_dict_with_ad_cols["targets"][1]["microhaplotypes"][0][
"pseudo_cigar"
] = "cigs"
rep_dict_with_ad_cols["targets"][1]["microhaplotypes"][1]["adcol1"] = "this"
rep_dict_with_ad_cols["targets"][1]["microhaplotypes"][1]["adcol2"] = "that"
rep_dict_with_ad_cols["targets"][1]["microhaplotypes"][1][
"pseudo_cigar"
] = "cigs"
rep_dict_with_ad_cols["targets"][2]["microhaplotypes"][0]["adcol1"] = "this"
rep_dict_with_ad_cols["targets"][2]["microhaplotypes"][0]["adcol2"] = "that"
rep_dict_with_ad_cols["targets"][2]["microhaplotypes"][0][
"pseudo_cigar"
] = "cigs"
rep_dict_with_ad_cols["targets"][2]["microhaplotypes"][1]["adcol1"] = "this"
rep_dict_with_ad_cols["targets"][2]["microhaplotypes"][1]["adcol2"] = "that"
rep_dict_with_ad_cols["targets"][2]["microhaplotypes"][1][
"pseudo_cigar"
] = "cigs"
for target in rep_dict_with_ad_cols["targets"]:
for mhap in target["microhaplotypes"]:
mhap["adcol1"] = "this"
mhap["adcol2"] = "that"

actual = create_representative_microhaplotype_dict(
mhap_table_ad_cols,
additional_representative_mhap_cols=["adcol1", "adcol2"],
pseudocigar_col="cig",
)
self.assertEqual(actual, rep_dict_with_ad_cols)

def test_create_representative_microhaplotype_dict_with_pseudocigar(self):
tbl = self.small_mhap_table.copy()
tbl["chrom"] = "chr1"
tbl["start"] = 100
tbl["end"] = 150
tbl["cig"] = "8M"
actual = create_representative_microhaplotype_dict(
tbl,
chrom_col="chrom",
start_col="start",
end_col="end",
pseudocigar_col="cig",
pseudocigar_start_col="start",
pseudocigar_end_col="end",
)
first = actual["targets"][0]["microhaplotypes"][0]
# pseudocigar is a Pseudocigar object with a GenomicLocation ref_loc;
# the chromosome is reused from chrom_col and genome_id defaults to 0
self.assertEqual(first["pseudocigar"]["pseudocigar_seq"], "8M")
self.assertEqual(
first["pseudocigar"]["ref_loc"],
{"genome_id": 0, "chrom": "chr1", "start": 100, "end": 150},
)

def test_pseudocigar_without_ref_loc_columns_raises(self):
tbl = self.small_mhap_table.copy()
tbl["cig"] = "8M"
with self.assertRaises(ValueError):
create_representative_microhaplotype_dict(tbl, pseudocigar_col="cig")

@patch(
"pmotools.pmo_builder.mhap_table_to_pmo.create_representative_microhaplotype_dict"
)
Expand Down
8 changes: 8 additions & 0 deletions tests/test_pmo_builder/test_schema_validation_integration.py
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Original file line number Diff line number Diff line change
Expand Up @@ -191,6 +191,8 @@ def test_full_1_0_0_toy_pmo_validates_against_schema():
umis_col="umis",
microhaplotype_name_col="microhap_name",
pseudocigar_col="pseudocigar",
pseudocigar_start_col="start",
pseudocigar_end_col="end",
quality_col="quality",
masking_seq_start_col="mask_start",
masking_seq_segment_size_col="mask_segment",
Expand Down Expand Up @@ -467,6 +469,9 @@ def test_slimer_1_1_0_toy_pmo_validates_against_schema():
"umis": [10],
"microhap_name": ["mh1"],
"pseudocigar": ["8M"],
"pseudocigar_chrom": ["chr1"],
"pseudocigar_start": [120],
"pseudocigar_end": [127],
"quality": ["ABCD"],
"mask_start": ["1"],
"mask_segment": ["2"],
Expand All @@ -480,6 +485,9 @@ def test_slimer_1_1_0_toy_pmo_validates_against_schema():
umis_col="umis",
microhaplotype_name_col="microhap_name",
pseudocigar_col="pseudocigar",
pseudocigar_chrom_col="pseudocigar_chrom",
pseudocigar_start_col="pseudocigar_start",
pseudocigar_end_col="pseudocigar_end",
quality_col="quality",
masking_seq_start_col="mask_start",
masking_seq_segment_size_col="mask_segment",
Expand Down
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