Raw content of Bio::EnsEMBL::IdMapping::StableIdGenerator::AedesAegypti
<![CDATA[=head1 LICENSE
Copyright (c) 1999-2009 The European Bioinformatics Institute and
Genome Research Limited. All rights reserved.
This software is distributed under a modified Apache license.
For license details, please see
/info/about/code_licence.html
=head1 CONTACT
Please email comments or questions to the public Ensembl
developers list at <ensembl-dev@ebi.ac.uk>.
Questions may also be sent to the Ensembl help desk at
<helpdesk@ensembl.org>.
=cut
package Bio::EnsEMBL::IdMapping::StableIdGenerator::AedesAegypti;
# Package that implements incrementing and verification of Aedes aegypti
# stable IDs as used by the VectorBase project.
# Based on Aedes_Aegypti.pm
# Differs from Aedes in that Exon stable ids like Ennnnnn not AAEL.ennnnnn
# and gene/transcript/translation start AGAP not AAEL
# also need to exclude old Ensembl-style ids
use strict;
use warnings;
use base qw(Bio::EnsEMBL::IdMapping::StableIdGenerator::EnsemblGeneric);
sub increment_stable_id {
# This method will increment a stable ID. For Anopheles, it will
# pick out the numerical part of the stable ID (no matter what type of
# stable ID it is) and increment it by one. It will then replace the
# numerical part by the incremented value and return the new stable
# ID. The parsing of the stable ID is very naive.
my ( $self, $stable_id ) = @_;
if ( !$self->is_valid($stable_id) ) {
throw("Unknown or missing stable ID: $stable_id.");
}
$stable_id =~ /^(\D*)(\d+)(\D*)/;
my $number_as_string = "$2";
my $number = $2 + 1;
$stable_id = sprintf(
"%s" . sprintf( "%%0%dd", length($number_as_string) ) . "%s",
$1, $number, $3 );
return $stable_id;
}
sub is_valid {
# A stable ID is a valid Anopheles stable ID if it begins with the
# character string "AGAP" or (for exons) just "E"
# explicitly make the exon one E+digits to exclude old-style ENSANG ids
# otherwise ENSANGnnn found as higher then AGAPnnn
# when initial_stable_id method checks archive tables
my ( $self, $stable_id ) = @_;
if ( !( defined($stable_id) && ( $stable_id =~ /^AGAP/ || $stable_id =~ /^E\d+$/ ) ) ) {
return 0;
}
return 1;
}
1;
]]>