From 39516de7d1423a853aaaa70061763600e1529c56 Mon Sep 17 00:00:00 2001
From: Martin Hammond <mh4@sanger.ac.uk>
Date: Thu, 23 Apr 2009 14:45:16 +0000
Subject: [PATCH] Add subclass of StableIdGenerator::EnsemblGeneric to do
Anopheles gambiae stable ID incrementation and verification.
---
.../StableIdGenerator/AnophelesGambiae.pm | 57 +++++++++++++++++++
1 file changed, 57 insertions(+)
create mode 100644 modules/Bio/EnsEMBL/IdMapping/StableIdGenerator/AnophelesGambiae.pm
diff --git a/modules/Bio/EnsEMBL/IdMapping/StableIdGenerator/AnophelesGambiae.pm b/modules/Bio/EnsEMBL/IdMapping/StableIdGenerator/AnophelesGambiae.pm
new file mode 100644
index 0000000000..366bb2c050
--- /dev/null
+++ b/modules/Bio/EnsEMBL/IdMapping/StableIdGenerator/AnophelesGambiae.pm
@@ -0,0 +1,57 @@
+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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