[ensembl-dev] fetch_transcript_by_display_label

Bob Stephens bob.stephens.2005 at gmail.com
Wed Nov 15 15:40:34 GMT 2017


Still getting familiar with the API so please excuse if this is an obvious
question. I want to retrieve all of the instances of a specific transcript
across species so I get the list of all available databases and then scan
for those with the group attribute of "core" and then use a transcript
adaptor connection to each database to see if a transcript is returned
matching the display label of "kras-202". It looks like any matches to eras
are returned as I get both kras-201 and kras-202  like sequences. (the
returned sequence display ids seem to be their stable_ids). The kras-201
transcripts are longer by 1 residue and so they are the ones included in
the ortholog family, but Id like to build an orthodox family for this
alternative transcript as well - any way to "force" it to return the
specific 202 form instead of the first one it encounters ? or do I need to
fetch all and then filter by length ? or by match to the human kras-202 for
example ? Is there a way to build my own orthologs family using a
non-longest transcript more generically ?

thanks for the help and the excellent access to the databases !

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