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src/cool_seq_tool/mappers/exon_genomic_coords.py

Lines changed: 2 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -840,6 +840,7 @@ async def _genomic_to_tx_segment(
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if not tx_exons:
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return GenomicTxSeg(errors=[f"No exons found given {transcript}"])
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# Determine if genomic_pos needs to be modified
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strand = Strand(tx_exons[0].alt_strand)
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params["strand"] = strand
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use_alt_start_i = self._use_alt_start_i(
@@ -848,7 +849,7 @@ async def _genomic_to_tx_segment(
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if use_alt_start_i and coordinate_type == CoordinateType.RESIDUE:
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genomic_pos = genomic_pos - 1 # Convert residue coordinate to inter-residue
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# gene is not required to liftover coordinates if tx_ac and genomic_ac are given, but we should set the associated gene
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# Extract gene symbol given transcript accession
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if not gene:
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_gene, err_msg = await self._get_tx_ac_gene(transcript)
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if err_msg:

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