[ensembl-dev] perl API: how to avoid deprecated identifiers?
myourshaw at g.ucla.edu
Mon Nov 3 02:09:09 GMT 2014
Apologies for sending this again, but the only ‘reply’ I got was a strange email from 'jv tra jurvin at gmail.com ‘ consisting solely of the text 'Hgpdna guanina tymine cysine adine ribose mitiohandrija skqi’. Looked like spam, or an accident.
At least with regard to mouse, GeneAdapter ->fetch_all() returns some genes with deprecated identifiers. For example, the mouse Acer2 gene has both ENSMUSG00000038007 and ENSMUSG00000091609.
Ensembl gene ENSMUSG00000091609 is no longer in the database but it has been mapped to 1 deprecated identifier . Not a Primary Assembly Gene.
Both the current and the deprecated genes have an is_current value of 1.
Although I have not checked them all manually, there appear to be 85 mouse genes with one or two such deprecated stable ids.
Is there a perl API way to fetch all genes and get only non-deprecated stable ids, or a method to detect and avoid them after fetching?
List of multiple Ensembl mouse stable ids associated with a single MGI gene symbol.
Michael Yourshaw, PhD
UCLA Geffen School of Medicine
Department of Pediatrics
695 Charles E Young Drive S
Los Angeles CA 90095-8348 USA
myourshaw at ucla.edu <mailto:myourshaw at ucla.edu>
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