fix(docs): Update get_genomic_tx_data function (#445)

closes #443

Author: jarbesfeld

src/cool_seq_tool/mappers/mane_transcript.py

@@ -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

src/cool_seq_tool/sources/uta_database.py

@@ -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.

tests/mappers/test_mane_transcript.py

@@ -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",

tests/sources/test_mane_transcript_mappings.py

@@ -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",
@@ -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",
@@ -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",
@@ -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",

tests/sources/test_uta_database.py

@@ -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,
@@ -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)