AnophelesGambiae.pm

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=cut
 
 
=head1 CONTACT
 
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=cut
 
package Bio::EnsEMBL::IdMapping::StableIdGenerator::AnophelesGambiae;
 
# 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;