Category: "Perl"

Proserver features

April 13th, 2008
When serving data in the DAS protocol using the Proserver, the features command will call a build_features function of the appropriate source adapter. It is passed one of: { 'segment' => $, 'start' => $, 'end' => $ } { 'feature_id' => $ }… more »

Perl Regex

March 6th, 2008
Some notes on using regular expressions to search / replace in Perl check for match: "Hello World" =~ m/World/; replace parts: $str = "Hello World"; $str =~ s/World/Moon/; Meta characters: \ Quote/Escape the next metacharacter ^ Match the beginning of… more »

Using BioMart

February 29th, 2008
Using the Biomart perl API check out code: cvs -d :pserver:cvsuser@cvs.sanger.ac.uk:/cvsroot/biomart login cvs -d :pserver:cvsuser@cvs.sanger.ac.uk:/cvsroot/biomart co -r release-0_6 biomart-perl configure: additional perl modules: CGI-Session,… more »

Different EnsEMBL routines

February 22nd, 2008
Useful bits of perl code to work with the EnsEMBL API Use the registry & get variation information: use Bio::EnsEMBL::Registry; my $reg = 'Bio::EnsEMBL::Registry'; my $host= 'ensembldb.ensembl.org'; my $user= 'anonymous'; $reg->load_re… more »

EnsEMBL db Installation

January 14th, 2008
A few notes about setting up a local EnsEMBL system (database and API) more »