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fix(docs): Update get_genomic_tx_data function #445

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Merged
jarbesfeld merged 2 commits into from
Dec 8, 2025
Merged

fix(docs): Update get_genomic_tx_data function #445

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324253a
Update docstring and modify test
jarbesfeld Dec 3, 2025
c3b8d1d
Update docstring and ensembl gene versions
jarbesfeld Dec 8, 2025
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2 changes: 1 addition & 1 deletion src/cool_seq_tool/mappers/mane_transcript.py
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Original file line number Diff line number Diff line change
Expand Up @@ -324,7 +324,7 @@ async def _get_and_validate_genomic_tx_data(
"""Get and validate genomic_tx_data

:param tx_ac: Accession on c. coordinate
:param pos: (start pos, end pos)
:param pos: (start pos, end pos). These are inter-residue coordinates
:param annotation_layer: Annotation layer for ``ac`` and ``pos``
:param coding_start_site: Coding start site
:param alt_ac: Accession on g. coordinate
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3 changes: 2 additions & 1 deletion src/cool_seq_tool/sources/uta_database.py
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Expand Up @@ -621,7 +621,8 @@ async def get_genomic_tx_data(
"""Get transcript mapping to genomic data.

:param tx_ac: Accession on c. coordinate
:param pos: (start pos, end pos)
:param pos: (start pos, end pos). These must describe the inter-residue
coordinates that are being examined.
:param annotation_layer: Annotation layer for ``ac`` and ``pos``
:param alt_ac: Accession on g. coordinate
:param target_genome_assembly: Genome assembly to get genomic data for.
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2 changes: 1 addition & 1 deletion tests/mappers/test_mane_transcript.py
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Expand Up @@ -32,7 +32,7 @@ def braf_mane_data():
"""Create test fixture for BRAF MANE data."""
return {
"#NCBI_GeneID": "GeneID:673",
"Ensembl_Gene": "ENSG00000157764.14",
"Ensembl_Gene": "ENSG00000157764.16",
"HGNC_ID": "HGNC:1097",
"symbol": "BRAF",
"name": "B-Raf proto-oncogene, serine/threonine kinase",
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8 changes: 4 additions & 4 deletions tests/sources/test_mane_transcript_mappings.py
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Expand Up @@ -13,7 +13,7 @@ def braf_select():
"""Create test fixture for BRAF MANE Select Transcript data."""
return {
"#NCBI_GeneID": "GeneID:673",
"Ensembl_Gene": "ENSG00000157764.14",
"Ensembl_Gene": "ENSG00000157764.16",
"HGNC_ID": "HGNC:1097",
"symbol": "BRAF",
"name": "B-Raf proto-oncogene, serine/threonine kinase",
Expand All @@ -34,7 +34,7 @@ def braf_plus_clinical():
"""Create test fixture for BRAF MANE Plus Clinical data."""
return {
"#NCBI_GeneID": "GeneID:673",
"Ensembl_Gene": "ENSG00000157764.14",
"Ensembl_Gene": "ENSG00000157764.16",
"HGNC_ID": "HGNC:1097",
"symbol": "BRAF",
"name": "B-Raf proto-oncogene, serine/threonine kinase",
Expand All @@ -55,7 +55,7 @@ def ercc6_plus_clinical():
"""Create test fixture for ERCC6 MANE Plus Clinical Transcript data."""
return {
"#NCBI_GeneID": "GeneID:2074",
"Ensembl_Gene": "ENSG00000225830.16",
"Ensembl_Gene": "ENSG00000225830.18",
"HGNC_ID": "HGNC:3438",
"symbol": "ERCC6",
"name": "ERCC excision repair 6, chromatin remodeling factor",
Expand All @@ -76,7 +76,7 @@ def ercc6_select():
"""Create test fixture for ERCC6 MANE Select Transcript data."""
return {
"#NCBI_GeneID": "GeneID:2074",
"Ensembl_Gene": "ENSG00000225830.16",
"Ensembl_Gene": "ENSG00000225830.18",
"HGNC_ID": "HGNC:3438",
"symbol": "ERCC6",
"name": "ERCC excision repair 6, chromatin remodeling factor",
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24 changes: 21 additions & 3 deletions tests/sources/test_uta_database.py
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Expand Up @@ -202,7 +202,25 @@ async def test_mane_c_genomic_data(test_db):
@pytest.mark.asyncio
async def test_get_genomic_tx_data(test_db, genomic_tx_data):
"""Test that get_genomic_tx_data works correctly."""
resp = await test_db.get_genomic_tx_data("NM_004333.4", (2145, 2145))
# Positive strand transcript
resp = await test_db.get_genomic_tx_data("NM_004327.3", (3595, 3596))
expected_params = {
"gene": "BCR",
"strand": Strand.POSITIVE,
"tx_pos_range": (3476, 3608),
"alt_pos_range": (23295023, 23295155),
"alt_aln_method": "splign",
"tx_exon_id": 956565,
"alt_exon_id": 6619783,
"tx_ac": "NM_004327.3",
"alt_ac": "NC_000022.11",
"pos_change": (119, 12),
"alt_pos_change_range": (23295142, 23295143),
}
assert resp == GenomicTxMetadata(**expected_params)

# Negative strand transcript
resp = await test_db.get_genomic_tx_data("NM_004333.4", (2144, 2145))
expected_params = {
"gene": "BRAF",
"strand": Strand.NEGATIVE,
Expand All @@ -213,8 +231,8 @@ async def test_get_genomic_tx_data(test_db, genomic_tx_data):
"alt_exon_id": 6619852,
"tx_ac": "NM_004333.4",
"alt_ac": "NC_000007.14",
"pos_change": (92, 43),
"alt_pos_change_range": (140739854, 140739854),
"pos_change": (91, 43),
"alt_pos_change_range": (140739855, 140739854),
}
assert resp == GenomicTxMetadata(**expected_params)

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