From 77fdbcf9efa2caa4ed89ae8bf820f4b3d82a8fa9 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andreas=20Kusalananda=20K=C3=A4h=C3=A4ri?=
<ak4@sanger.ac.uk>
Date: Mon, 19 Mar 2012 12:28:59 +0000
Subject: [PATCH] In filter_biotypes():
If the configuration parameter 'not_biotypes' is present, exclude all
genes whose biotype is listed (but include all other genes).
If the configuration parameter 'biotypes' is present, include all
genes whose biotype is listed (as usual).
It is an error to define both options in the configuration.
---
modules/Bio/EnsEMBL/IdMapping/Cache.pm | 64 ++++++++++++++++++++++----
1 file changed, 55 insertions(+), 9 deletions(-)
diff --git a/modules/Bio/EnsEMBL/IdMapping/Cache.pm b/modules/Bio/EnsEMBL/IdMapping/Cache.pm
index d67ec2b042..a6768f1171 100644
--- a/modules/Bio/EnsEMBL/IdMapping/Cache.pm
+++ b/modules/Bio/EnsEMBL/IdMapping/Cache.pm
@@ -404,8 +404,21 @@ sub build_cache_from_genes {
Arg[1] : Listref of Bio::EnsEMBL::Genes $genes - the genes to filter
Example : my @filtered = @{ $cache->filter_biotypes(\@genes) };
- Description : Filters a list of genes by biotype. Biotypes are taken from the
- IdMapping configuration parameter 'biotypes'.
+
+ Description : Filters a list of genes by biotype. Biotypes are
+ taken from the IdMapping configuration parameter
+ 'biotypes' or 'not_biotypes'.
+
+ If the configuration parameter 'not_biotypes' is
+ defined, then rather than returning the genes whose
+ biotype is listed in the configuration parameter
+ 'biotypes' the method will return the genes whose
+ biotype is *not* listed in the 'not_biotypes'
+ configuration parameter.
+
+ It is an error to define both these configuration
+ parameters.
+
Return type : Listref of Bio::EnsEMBL::Genes (or empty list)
Exceptions : none
Caller : internal
@@ -415,17 +428,50 @@ sub build_cache_from_genes {
=cut
sub filter_biotypes {
- my $self = shift;
- my $genes = shift;
+ my ( $self, $genes ) = @_;
- my $filtered = [];
+ my @filtered;
+ my @biotypes;
+ my $opt_reverse;
- foreach my $biotype ($self->conf->param('biotypes')) {
- push @$filtered, grep { $_->biotype eq $biotype } @$genes;
+ if ( defined( $self->conf()->param('biotypes') ) ) {
+ if ( defined( $self->conf()->param('not_biotypes') ) ) {
+ $self->logger()
+ ->error( "You may not use both 'biotypes' and 'not_biotypes' " .
+ "in the configuration" );
+ }
+
+ @biotypes = $self->conf()->param('biotypes');
+ $opt_reverse = 0;
+ }
+ else {
+ @biotypes = $self->conf()->param('not_biotypes');
+ $opt_reverse = 1;
}
- return $filtered;
-}
+ foreach my $gene ( @{$genes} ) {
+ my $keep_gene;
+
+ foreach my $biotype (@biotypes) {
+ if ( $gene->biotype() eq $biotype ) {
+ if ($opt_reverse) { $keep_gene = 0 }
+ else { $keep_gene = 1 }
+ last;
+ }
+ }
+
+ if ( defined($keep_gene) ) {
+ if ($keep_gene) {
+ push( @filtered, $gene );
+ }
+ }
+ elsif ($opt_reverse) {
+ push( @filtered, $gene );
+ }
+ }
+
+ return \@filtered;
+} ## end sub filter_biotypes
=head2 add
--
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