feat: get cds overlap given chromosome, start, + stop #217
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| identifier: Optional[str] = None, | ||
| residue_mode: ResidueMode = ResidueMode.RESIDUE, | ||
| ) -> Optional[Dict]: | ||
| """Get feature overlap for GRCh38 genomic data |
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Would someone (Kori? @austinant?) be willing -- for my sake -- to add a descriptive sentence or two here? I can also paraphrase something from the manuscript if there's a specific relevant section
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(still a mess but hopefully more descriptive)
For input CNV, specified as a sequence location by chromosome, start, stop, this function returns all coding exons (CDS regions) with which the variant has nonzero base pair overlap. Result is a dictionary keyed by genes which overlap with the input variant, mapping to a list of the overlapping exons in each gene with the beginning and end of the variant's overlap with each.
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@jsstevenson updated. Let me know if that clears things up for you
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@austinant how about
"""Given GRCh38 genomic data, find the overlapping MANE features (gene and cds).
The genomic data is specified as a sequence location by `chromosome`, `start`,
`end`. All CDS regions with which the input sequence location has nonzero base
pair overlap will be returned.
:return: MANE feature (gene/cds) overlap data represented as a dict. The
dictionary will be keyed by genes which overlap the input sequence location.
Each gene contains a list of the overlapping CDS regions with the beginning
and end of the input sequence location's overlap with each
{
gene: {
'cds': VRS Sequence Location
'overlap': VRS Sequence Location
}
}
"""
vrs seq loc, inter-residue, docstring
|
Need to look over this with fresh brain/eyes before re-requesting reviews |
Ready for review! |
|
Good catch @ahwagner |
| identifier: Optional[str] = None, | ||
| residue_mode: ResidueMode = ResidueMode.RESIDUE, | ||
| ) -> Optional[Dict]: | ||
| """Get feature overlap for GRCh38 genomic data |
There was a problem hiding this comment.
(still a mess but hopefully more descriptive)
For input CNV, specified as a sequence location by chromosome, start, stop, this function returns all coding exons (CDS regions) with which the variant has nonzero base pair overlap. Result is a dictionary keyed by genes which overlap with the input variant, mapping to a list of the overlapping exons in each gene with the beginning and end of the variant's overlap with each.
Address #216 for 0.1.x . This is needed for variation manuscript
Notes:
FeatureOverlap) for getting cds overlapget_mane_summary-->get_mane