[Bioperl-l] Gbrowse/BioSQL question

Marc Logghe Marc.Logghe at devgen.com
Wed May 5 16:24:29 EDT 2004

Hi Sean,
I did not find a way to pass multiple version numbers neither. Because in the back a find_by_unique_key is performed and *NOT* a find_by_query. Meaning, you need to pass a version *and* an accession number. The accession number is passed via the gbrowse interface, the version is fixed in the configuration file. 
THe workaround we are currently using is to set the version field to 0 for all the bioentries at the database level. Really dirty and too bad when you have different versions of the same entry :(
I tried to set version to % in the hope that somewhere in the select query 'version like %' will be called but alas.
BTW, this seems to work fine for the namespace ! You can query multiple namespaces for a certain accession by setting biodbname to % in the conf file.


-----Original Message-----
From: Sean Davis [mailto:sdavis2 at mail.nih.gov]
Sent: Wednesday, May 05, 2004 9:32 PM
To: Bioperl
Subject: [Bioperl-l] Gbrowse/BioSQL question

Dear all,

In the Gbrowse configuration file when using BioSQL as the underlying
database schema, there is a requirement for version to be identified.  I
have loaded refSeq and would like to use Gbrowse to browse the entries, but,
of course, there are varying version numbers in the current refSeq file, so
I can only search a subset at any given time.  Is there a way to deal with
this issue so that one can include multiple version numbers in the default
for searching?


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