[ensembl-dev] ensembl blast problem

Sharon Wei weix at cshl.edu
Wed Feb 12 18:44:28 GMT 2014


Dear Ensembl Blastview developers,

There seem to be a problem with ensembl blast url 
http://useast.ensembl.org/Multi/blastview. If you blast against a non 
primary species database such a Zea_mays in the case of ensembl plants, 
you would get a blast ticket. However typing in the same ticket url (for 
example: http://plants.ensembl.org/Multi/blastview/BLA_DTqOPD0X6) in 
another tab, you would always get blast results against Oryza_sativa ie, 
the default primary species. Checking in the blastview code, I found the 
codes similar to the following that explain the behavior. However I am 
wondering whether it would make more sense to look in the blast database 
with the ticket token before assigning ensembl species

my $tsp = $ENV{'ENSEMBL_SPECIES'} eq 'Multi' ? 
$SPECIES_DEFS->ENSEMBL_PRIMARY_SPECIES : $ENV{'ENSEMBL_SPECIES'};

  Thanks,

Sharon




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