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feat!: Add strand in GenomicTxSeg output #408

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Merged
jarbesfeld merged 1 commit into from
Jun 23, 2025
Merged

feat!: Add strand in GenomicTxSeg output #408

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12 changes: 12 additions & 0 deletions src/cool_seq_tool/mappers/exon_genomic_coords.py
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Original file line number Diff line number Diff line change
Expand Up @@ -93,6 +93,9 @@ class GenomicTxSeg(BaseModelForbidExtra):
)
genomic_ac: StrictStr | None = Field(None, description="RefSeq genomic accession.")
tx_ac: StrictStr | None = Field(None, description="RefSeq transcript accession.")
strand: Strand | None = Field(
None, description="The strand that the transcript accession exists on."
)
errors: list[StrictStr] = Field([], description="Error messages.")

@model_validator(mode="before")
Expand Down Expand Up @@ -121,6 +124,7 @@ def check_errors(cls, values: dict) -> dict: # noqa: N805
"gene": "TPM3",
"genomic_ac": "NC_000001.11",
"tx_ac": "NM_152263.3",
"strand": -1,
"seg": {
"exon_ord": 0,
"offset": 0,
Expand All @@ -147,6 +151,9 @@ class GenomicTxSegService(BaseModelForbidExtra):
)
genomic_ac: StrictStr | None = Field(None, description="RefSeq genomic accession.")
tx_ac: StrictStr | None = Field(None, description="RefSeq transcript accession.")
strand: Strand | None = Field(
None, description="The strand that the transcript exists on."
)
seg_start: TxSegment | None = Field(None, description="Start transcript segment.")
seg_end: TxSegment | None = Field(None, description="End transcript segment.")
errors: list[StrictStr] = Field([], description="Error messages.")
Expand Down Expand Up @@ -183,6 +190,7 @@ def add_meta_check_errors(cls, values: dict) -> dict: # noqa: N805
"gene": "TPM3",
"genomic_ac": "NC_000001.11",
"tx_ac": "NM_152263.3",
"strand": -1,
"seg_start": {
"exon_ord": 0,
"offset": 0,
Expand Down Expand Up @@ -400,6 +408,7 @@ async def tx_segment_to_genomic(
gene=gene,
genomic_ac=genomic_ac,
tx_ac=transcript,
strand=strand,
seg_start=seg_start,
seg_end=seg_end,
)
Expand Down Expand Up @@ -490,6 +499,7 @@ async def genomic_to_tx_segment(
params["gene"] = start_tx_seg_data.gene
params["genomic_ac"] = start_tx_seg_data.genomic_ac
params["tx_ac"] = start_tx_seg_data.tx_ac
params["strand"] = start_tx_seg_data.strand
params["seg_start"] = start_tx_seg_data.seg
else:
start_tx_seg_data = None
Expand Down Expand Up @@ -524,6 +534,7 @@ async def genomic_to_tx_segment(
params["gene"] = end_tx_seg_data.gene
params["genomic_ac"] = end_tx_seg_data.genomic_ac
params["tx_ac"] = end_tx_seg_data.tx_ac
params["strand"] = end_tx_seg_data.strand

params["seg_end"] = end_tx_seg_data.seg

Expand Down Expand Up @@ -902,6 +913,7 @@ async def _genomic_to_tx_segment(
gene=gene,
genomic_ac=genomic_ac,
tx_ac=transcript,
strand=strand,
seg=TxSegment(
exon_ord=exon_num,
offset=offset,
Expand Down
21 changes: 21 additions & 0 deletions tests/mappers/test_exon_genomic_coords.py
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Original file line number Diff line number Diff line change
Expand Up @@ -171,6 +171,7 @@ def tpm3_exon1():
"gene": "TPM3",
"genomic_ac": "NC_000001.11",
"tx_ac": "NM_152263.3",
"strand": -1,
"seg": {
"exon_ord": 0,
"offset": 0,
Expand All @@ -194,6 +195,7 @@ def tpm3_exon8():
"gene": "TPM3",
"genomic_ac": "NC_000001.11",
"tx_ac": "NM_152263.3",
"strand": -1,
"seg": {
"exon_ord": 7,
"offset": 0,
Expand All @@ -217,6 +219,7 @@ def tpm3_exon1_g(tpm3_exon1):
"gene": tpm3_exon1.gene,
"genomic_ac": tpm3_exon1.genomic_ac,
"tx_ac": tpm3_exon1.tx_ac,
"strand": tpm3_exon1.strand,
"seg_start": tpm3_exon1.seg,
}
return GenomicTxSegService(**params)
Expand All @@ -229,6 +232,7 @@ def tpm3_exon8_g(tpm3_exon8):
"gene": tpm3_exon8.gene,
"genomic_ac": tpm3_exon8.genomic_ac,
"tx_ac": tpm3_exon8.tx_ac,
"strand": tpm3_exon8.strand,
"seg_end": tpm3_exon8.seg,
}
return GenomicTxSegService(**params)
Expand All @@ -241,6 +245,7 @@ def tpm3_exon1_exon8(tpm3_exon1, tpm3_exon8):
"gene": tpm3_exon8.gene,
"genomic_ac": tpm3_exon8.genomic_ac,
"tx_ac": tpm3_exon8.tx_ac,
"strand": tpm3_exon8.strand,
"seg_start": tpm3_exon1.seg,
"seg_end": tpm3_exon8.seg,
}
Expand All @@ -261,6 +266,7 @@ def tpm3_exon1_exon8_offset(tpm3_exon1, tpm3_exon8):
"gene": "TPM3",
"genomic_ac": "NC_000001.11",
"tx_ac": "NM_152263.3",
"strand": -1,
"seg_start": tpm3_exon1_cpy.seg,
"seg_end": tpm3_exon8_cpy.seg,
}
Expand All @@ -274,6 +280,7 @@ def mane_braf():
"gene": "BRAF",
"genomic_ac": "NC_000007.14",
"tx_ac": "NM_004333.6",
"strand": -1,
"seg_start": {
"exon_ord": 5,
"offset": 1,
Expand Down Expand Up @@ -309,6 +316,7 @@ def wee1_exon2_exon11():
"gene": "WEE1",
"genomic_ac": "NC_000011.10",
"tx_ac": "NM_003390.3",
"strand": 1,
"seg_start": {
"exon_ord": 1,
"offset": 205,
Expand Down Expand Up @@ -344,6 +352,7 @@ def mane_wee1_exon2_exon11():
"gene": "WEE1",
"genomic_ac": "NC_000011.10",
"tx_ac": "NM_003390.4",
"strand": 1,
"seg_start": {
"exon_ord": 1,
"offset": 205,
Expand Down Expand Up @@ -379,6 +388,7 @@ def ntrk1_exon10_exon17():
"gene": "NTRK1",
"genomic_ac": "NC_000001.11",
"tx_ac": "NM_002529.3",
"strand": 1,
"seg_start": {
"exon_ord": 9,
"offset": 0,
Expand Down Expand Up @@ -414,6 +424,7 @@ def zbtb10_exon3_end():
"gene": "ZBTB10",
"genomic_ac": "NC_000008.11",
"tx_ac": "NM_001105539.3",
"strand": 1,
"seg_start": None,
"seg_end": {
"exon_ord": 2,
Expand All @@ -438,6 +449,7 @@ def zbtb10_exon5_start():
"gene": "ZBTB10",
"genomic_ac": "NC_000008.11",
"tx_ac": "NM_001105539.3",
"strand": 1,
"seg_start": {
"exon_ord": 4,
"offset": -201,
Expand All @@ -462,6 +474,7 @@ def tpm3_exon6_end():
"gene": "TPM3",
"genomic_ac": "NC_000001.11",
"tx_ac": "NM_152263.4",
"strand": -1,
"seg_start": None,
"seg_end": {
"exon_ord": 5,
Expand All @@ -486,6 +499,7 @@ def tpm3_exon5_start():
"gene": "TPM3",
"genomic_ac": "NC_000001.11",
"tx_ac": "NM_152263.4",
"strand": -1,
"seg_start": {
"exon_ord": 4,
"offset": -102,
Expand All @@ -510,6 +524,7 @@ def gusbp3_exon2_end():
"gene": "GUSBP3",
"genomic_ac": "NC_000005.10",
"tx_ac": "NR_027386.2",
"strand": -1,
"seg_start": None,
"seg_end": {
"exon_ord": 1,
Expand All @@ -534,6 +549,7 @@ def eln_grch38_intronic():
"gene": "ELN",
"genomic_ac": "NC_000007.14",
"tx_ac": "NM_000501.4",
"strand": 1,
"seg_start": {
"exon_ord": 0,
"offset": 1,
Expand Down Expand Up @@ -569,6 +585,7 @@ def gusbp3_exon5_start():
"gene": "GUSBP3",
"genomic_ac": "NC_000005.10",
"tx_ac": "NR_027386.2",
"strand": -1,
"seg_start": {
"exon_ord": 4,
"offset": -3589,
Expand Down Expand Up @@ -609,6 +626,7 @@ def genomic_tx_seg_service_checks(actual, expected=None, is_valid=True):
assert actual.gene == expected.gene
assert actual.genomic_ac == expected.genomic_ac
assert actual.tx_ac == expected.tx_ac
assert actual.strand == expected.strand

for seg_attr in ["seg_start", "seg_end"]:
expected_seg = getattr(expected, seg_attr)
Expand All @@ -635,6 +653,7 @@ def genomic_tx_seg_service_checks(actual, expected=None, is_valid=True):
assert actual.gene is None
assert actual.genomic_ac is None
assert actual.tx_ac is None
assert actual.strand is None
assert actual.seg_start is None
assert actual.seg_end is None
assert len(actual.errors) > 0
Expand Down Expand Up @@ -678,6 +697,7 @@ def genomic_tx_seg_checks(actual, expected=None, is_valid=True):
assert actual.gene == expected.gene
assert actual.genomic_ac == expected.genomic_ac
assert actual.tx_ac == expected.tx_ac
assert actual.strand == expected.strand

expected_seg = expected.seg
if expected_seg:
Expand All @@ -700,6 +720,7 @@ def genomic_tx_seg_checks(actual, expected=None, is_valid=True):
assert actual.gene is None
assert actual.genomic_ac is None
assert actual.tx_ac is None
assert actual.strand is None
assert actual.seg is None
assert len(actual.errors) > 0

Expand Down