[ensembl-dev] Question regarding transcript location data

[Duarte Molha]

Dear developers

I have a script that retrieves intron and exon information from an input NM ID. It is working pretty well but I have stumbled on a few NM iDS and I would like to know what I can to correct the behaviour of the script.

As an example if I input this ID:

NM_173471

My script ouputs:

INPUT_ID            CHR                                        start                       end                        ENST_ID                               EXON_ID                             strand
NM_173471       chrHG991_PATCH              66119285            66119659             ENST00000566782            ENSE00002619671 0         +1
NM_173471       chrHG991_PATCH              66298434            66298819             ENST00000566782            ENSE00002619173 0         +1
... <abbreviated>

However what I would have liked to have been outputted was the correct genomic location of this transcript... in this case chr3.
Can you tell me how I can change by script so that it gets the correct chr location instead of this PATCH ids?

Basically I would have wanted the script to have outputted the exon/intron data from the first entry on this link:

http://www.ensembl.org/Homo_sapiens/Search/Details?species=Homo_sapiens;idx=Transcript;end=2;q=NM_173471


Best regards,

Duarte Molha

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