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Remove transcript "variant X" when transferring to genes #373

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May 23, 2024
Merged

Remove transcript "variant X" when transferring to genes #373

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Remove transcript "variant X" when transferring to genes
MatBarba May 22, 2024
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MatBarba May 23, 2024
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8 changes: 8 additions & 0 deletions src/python/ensembl/io/genomio/gff3/extract_annotation.py
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Original file line number Diff line number Diff line change
Expand Up @@ -230,13 +230,21 @@ def _transfer_description_up(self, child_feature: str) -> None:
for child_id, child in children_features.items():
child_description = child.get("description")
if child_description is not None:
child_description = self._clean_description(child_description)
# Check parent
parent_id = self.get_parent(parent_type, child_id)
parent = parent_features[parent_id]
parent_description = parent.get("description")
if parent_description is None:
parent["description"] = child_description

@staticmethod
def _clean_description(description: str) -> str:
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"""Returns the description without "transcript variant" information."""
variant_re = re.compile(r", transcript variant [A-Z][0-9]+$", re.IGNORECASE)
description = re.sub(variant_re, "", description)
return description

@staticmethod
def product_is_informative(product: str, feat_ids: Optional[List[str]] = None) -> bool:
"""Returns True if the product name contains informative words, False otherwise.
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24 changes: 16 additions & 8 deletions src/python/tests/gff3/test_extract_annotation.py
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Expand Up @@ -312,14 +312,22 @@ def test_get_features(feat_type: str, expected_number: int, expected: ContextMan
@pytest.mark.parametrize(
"gene_desc, transc_desc, transl_desc, out_gene_desc, out_transc_desc",
[
(None, None, None, None, None),
("Foobar", None, None, "Foobar", None), # Only gene descriptions
("gene A", "transc B", "prod C", "gene A", "transc B"), # All descriptions set
(None, None, "Foobar", "Foobar", "Foobar"), # Transfer from transl
(None, "Foobar", None, "Foobar", "Foobar"), # Transfer from transc
(None, "Foobar", "Lorem", "Foobar", "Foobar"), # Transfer from transc, transl also set
("Hypothetical gene", "Predicted function", "Foobar", "Foobar", "Foobar"), # Non informative
(None, None, "Unknown product", None, None), # Non informative source
param(None, None, None, None, None, id="Nothing provided"),
param("Foobar", None, None, "Foobar", None, id="Only gene description"),
param("gene A", "transc B", "prod C", "gene A", "transc B", id="All descriptions set"),
param(None, None, "Foobar", "Foobar", "Foobar", id="Transfer from transl"),
param(None, "Foobar", None, "Foobar", "Foobar", id="Transfer from transc"),
param(
None,
"Foobar, transcript variant X1",
None,
"Foobar",
"Foobar, transcript variant X1",
id="transcr with variant",
),
param(None, "Foobar", "Lorem", "Foobar", "Foobar", id="Transfer from transc, transl also set"),
param("Hypothetical gene", "Predicted function", "Foobar", "Foobar", "Foobar", id="Non informative"),
param(None, None, "Unknown product", None, None, id="Non informative source"),
],
)
@pytest.mark.dependency(depends=["get_features"])
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