From ff5dbe266c60f6a855b6b118a8e37ea4ce722b1f Mon Sep 17 00:00:00 2001
From: Web Group <www-ens@sanger.ac.uk>
Date: Mon, 17 Dec 2012 12:28:22 +0000
Subject: [PATCH] Copy is_patch onto branch 66 now that anacode have moved on.
-- ds23
---
.../Bio/EnsEMBL/Utils/ConversionSupport.pm | 25 +++++++++++++++++++
1 file changed, 25 insertions(+)
diff --git a/modules/Bio/EnsEMBL/Utils/ConversionSupport.pm b/modules/Bio/EnsEMBL/Utils/ConversionSupport.pm
index bdfcfd1555..6eb8d9e14d 100644
--- a/modules/Bio/EnsEMBL/Utils/ConversionSupport.pm
+++ b/modules/Bio/EnsEMBL/Utils/ConversionSupport.pm
@@ -1194,6 +1194,31 @@ sub split_chromosomes_by_size {
return $chr_slices;
}
+=head2 is_patch
+
+ Arg[1] : B::E::Slice
+ Example : if ($support->is_patch($slice)) { ...
+ Description : Looks at seq_region attributes to decide if a slice is a patch or not
+ If PATCH seq_region_attrib is not there check to see if name suggests it is a PATCH
+ Return type : true/false
+
+=cut
+
+sub is_patch {
+ my ($self,$slice) = @_;
+ my @patch_attrib_types = qw(patch_fix patch_novel); #seq_region_attribs used to define a patch
+ foreach my $attrib_type (@patch_attrib_types) {
+ if (@{$slice->get_all_Attributes($attrib_type)}) {
+ return 1;
+ }
+ }
+ if ($slice->seq_region_name =~ /PATCH/) {
+ $self->log_warning($slice->seq_region_name . " has a PATCH name does not have a patch seq_region_attrib, please check if it was present in loutre\n");
+ return 1;
+ }
+ return 0;
+}
+
=head2 log
Arg[1] : String $txt - the text to log
--
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