Disha/primary transc fix #358
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MatBarba
approved these changes
May 9, 2024
| @@ -457,7 +457,7 @@ def normalize_mirna(self, gene: SeqFeature) -> List[SeqFeature]: | |||
| """Returns gene representations from a miRNA gene that can be loaded in an Ensembl database. | |||
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| Change the representation from the form `gene[ primary_transcript[ exon, miRNA[ exon ] ] ]` | |||
| to `gene[ primary_transcript[ exon ] ]` and `gene[ miRNA[ exon ] ]` | |||
| to `gene[ miRNA_primary_transcript[ exon ] ]` and `gene[ miRNA[ exon ] ]` | |||
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Suggested change
| to `gene[ miRNA_primary_transcript[ exon ] ]` and `gene[ miRNA[ exon ] ]` | |
| to `ncRNA_gene[ miRNA_primary_transcript[ exon ] ]` and `gene[ miRNA[ exon ] ]` |
| logging.debug(f"Formatting miRNA gene {gene.id}") | ||
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| new_genes = [] | ||
| new_primary_subfeatures = [] | ||
| num = 1 | ||
| for sub in primary.sub_features: | ||
| if sub.type == "exon": | ||
| gene.type = "ncRNA_gene" | ||
| primary.type = "miRNA_primary_transcript" | ||
| new_primary_subfeatures.append(sub) |
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I would put the biotype change at the earlier stage where we create the primary and the gene (472-473)
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oh yes makes sense ! I have forgotten to make that change.
Comment on lines
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| does_not_raise(), | ||
| id="gene + primary_transcript + miRNA", | ||
| id="ncRNA_gene + miRNA_primary_transcript + miRNA", | ||
| ), | ||
| param( | ||
| "mirna/pseudogene.gff", | ||
| "mirna/pseudogene_simped.gff", | ||
| does_not_raise(), | ||
| id="gene + primary_transcript - miRNA", | ||
| id="ncRNA_gene + miRNA_primary_transcript - miRNA", | ||
| ), | ||
| param( | ||
| "mirna/nogene.gff", | ||
| "mirna/nogene_simped.gff", | ||
| does_not_raise(), | ||
| id="primary_transcript + miRNA", | ||
| id="miRNA_primary_transcript + miRNA", | ||
| ), | ||
| param( | ||
| "mirna/pseudo_nogene.gff", | ||
| "mirna/pseudo_nogene_simped.gff", | ||
| does_not_raise(), | ||
| id="primary_transcript - miRNA", | ||
| id="miRNA_primary_transcript - miRNA", | ||
| ), | ||
| param( | ||
| "mirna/unsupported_tr.gff", | ||
| "", | ||
| raises(GFFParserError, match="Unknown subtype"), | ||
| id="gene + primary_transcript + mRNA, not supported", | ||
| id="ncRNA_gene + miRNA_primary_transcript + mRNA, not supported", | ||
| ), | ||
| param( | ||
| "mirna/two_primary.gff", | ||
| "", | ||
| raises(GFFParserError, match="too many sub_features"), | ||
| id="gene + 2x primary_transcript, not supported", | ||
| id="gene + 2x miRNA_primary_transcript, not supported", | ||
| ), |
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Here I would keep the old names, because they correspond to the input biotypes, not the results (the input files have not changed)
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I have changed the biotype for primary transcript --> miRNA_primary_transcript and the associated gene --> ncRNA_gene for loading them correctly.