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GenomicMedLab / cool-seq-tool

https://coolseqtool.readthedocs.io
MIT License
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MANE transcript data was not found for the gene C1orf159 #367

Open jarbesfeld opened 3 weeks ago

jarbesfeld commented 3 weeks ago

Describe the bug

When using the genomic_to_tx_segment method in cool-seq-tool, it returned an error stating that MANE transcript data could not be found for the gene C1orf159. However, there is a MANE transcript: https://www.ncbi.nlm.nih.gov/nuccore/NM_017891.

Steps to reproduce

await self.fusor.transcript_segment_element(
            tx_to_genomic_coords=False,
            chromosome=1,
            seg_end_genomic=1098742,
            gene="C1orf159",
            get_nearest_transcript_junction=True,
        )

Expected behavior

The transcript NM_017891.5 would be selected

Current behavior

The following statement is outputted: Unable to get MANE Transcript data for gene: C1ORF159

Possible reason(s)

No response

Suggested fix

No response

Branch, commit, and/or version

Main branch

Screenshots

No response

Environment details

Mac M1

Additional details

No response

Contribution

None

korikuzma commented 3 weeks ago

@jarbesfeld can you let me know what is passed to cool-seq-tool?

korikuzma commented 3 weeks ago

I think it's just g -> tx seg with the values not changing, but want to confirm.

jarbesfeld commented 3 weeks ago

@korikuzma I think the input that is passed to cool-seq-tool is:

genomic_to_tx_segment(
        chromosome = 1,
        seg_end_genomic=1098742,
        gene="C1orf159",
        get_nearest_transcript_junction=True,
)
korikuzma commented 1 week ago

I will investigate this next sprint