get_coordinates_from_exon_id() <enhancement>

[alec-djinn]

@iskandr Is there a way to get the coordinates of a given exon_id? If not, it would be very useful to have it as enhancement.

[tavinathanson]

@alec-djinn does this meet your needs?

exon = ensembl_release.exon_by_id(exon_id)
coordinates = (exon.contig, exon.start, exon.end)

[alec-djinn]

Yes! It's exactly what I was looking for. Although, the returned exon.start and exon.end value are probably sorted (start is always smaller than end) and do not take into account the orientation of the gene. for example:

from pyensembl import EnsemblRelease
data = EnsemblRelease(75)
exon = data.exon_by_id('ENSE00002051192')
coordinates = (exon.contig, exon.start, exon.end)

>>> coordinates
>>> ('17', 7590695, 7590799)

While if you check on the Ensembl website: http://grch37.ensembl.org/Homo_sapiens/Transcript/Exons?db=core;g=ENSG00000141510;r=17:7565097-7590856;t=ENST00000420246

No.	Exon/Intron	Start	End
1	ENSE00002051192	7,590,799	7,590,695

[tavinathanson]

@alec-djinn how about exon.strand?

[alec-djinn]

Sure, I can use that as well. Thanks!

[tavinathanson]

Cool, closing this issue since it seems resolved.