renaming chromosome to genomic_ac for consistency with cool-seq-tool

cancervariants · Aug 21, 2024 · 00ed45f · 00ed45f
1 parent 3a06f55
commit 00ed45f
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Showing 2 changed files with 7 additions and 9 deletions.
diff --git a/src/fusor/fusor.py b/src/fusor/fusor.py
@@ -257,15 +257,13 @@ async def transcript_segment_element(
                 **kwargs
             )
         else:
-            if "chromosome" in kwargs and kwargs.get("chromosome") is None:
+            if "genomic_ac" in kwargs and kwargs.get("genomic_ac") is None:
                 msg = (
-                    "`chromosome` is required when going from genomic to"
+                    "`genomic_ac` is required when going from genomic to"
                     " transcript exon coordinates"
                 )
                 _logger.warning(msg)
                 return None, [msg]
-            chromosome = kwargs.get("chromosome")
-            kwargs["genomic_ac"] = chromosome
             data = await self.cool_seq_tool.ex_g_coords_mapper.genomic_to_tx_segment(
                 **kwargs
             )

diff --git a/tests/test_fusor.py b/tests/test_fusor.py
@@ -438,7 +438,7 @@ async def test_transcript_segment_element(
         transcript="NM_152263.3",
         seg_start_genomic=154192135,
         seg_end_genomic=154170399,
-        chromosome="NC_000001.11",
+        genomic_ac="NC_000001.11",
         tx_to_genomic_coords=False,
     )
     assert tsg[0]
@@ -488,7 +488,7 @@ async def test_transcript_segment_element(
         transcript="NM_152263.3",
         seg_start_genomic=154192135,
         seg_end_genomic=154170399,
-        chromosome="NC_000001.11",
+        genomic_ac="NC_000001.11",
         tx_to_genomic_coords=False,
         seq_id_target_namespace="ga4gh",
     )
@@ -520,7 +520,7 @@ async def test_transcript_segment_element(
         transcript="NM_152263.3",
         seg_start_genomic=154192135,
         seg_end_genomic=154170404,
-        chromosome="NC_000001.11",
+        genomic_ac="NC_000001.11",
         tx_to_genomic_coords=False,
         seq_id_target_namespace="ga4gh",
     )
@@ -547,7 +547,7 @@ async def test_transcript_segment_element(
     tsg = await fusor_instance.transcript_segment_element(
         transcript="NM_152263.3",
         seg_start_genomic=154192135,
-        chromosome="NC_000001.11",
+        genomic_ac="NC_000001.11",
         tx_to_genomic_coords=False,
         seq_id_target_namespace="ga4gh",
     )
@@ -558,7 +558,7 @@ async def test_transcript_segment_element(
     # MANE
     tsg = await fusor_instance.transcript_segment_element(
         tx_to_genomic_coords=False,
-        chromosome="NC_000011.10",
+        genomic_ac="NC_000011.10",
         seg_start_genomic=9575887,
         gene="WEE1",
     )