Commit 39516de7 authored by Martin Hammond's avatar Martin Hammond
Browse files

Add subclass of StableIdGenerator::EnsemblGeneric to do Anopheles gambiae...

Add subclass of StableIdGenerator::EnsemblGeneric to do Anopheles gambiae stable ID incrementation and verification.
parent 441627a1
package Bio::EnsEMBL::IdMapping::StableIdGenerator::AnophelesGambiae;
# Package that implements incrementing and verification of Anopheles gambiae
# 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 needs to explicitly exclude old-style ids, as base will look at gene_archve and will consider ENSANGG to be a higher id than any AGAP, so will use that as starting pint fornew 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"
# must make the exon one explicityly E+digits, so that will exclude old-style ENSANG ids
# otherwise these cause problems 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;
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