From 9ce56e57e55bd625f9f861701acef508ab04574a Mon Sep 17 00:00:00 2001
From: Magali Ruffier <mr6@ebi.ac.uk>
Date: Thu, 1 Nov 2012 09:32:21 +0000
Subject: [PATCH] pig is a merged species, needs some special methods to
overwrite the default ones
---
.../xref_mapping/XrefMapper/sus_scrofa.pm | 82 +++++++++++++++++++
1 file changed, 82 insertions(+)
create mode 100644 misc-scripts/xref_mapping/XrefMapper/sus_scrofa.pm
diff --git a/misc-scripts/xref_mapping/XrefMapper/sus_scrofa.pm b/misc-scripts/xref_mapping/XrefMapper/sus_scrofa.pm
new file mode 100644
index 0000000000..d697c2c636
--- /dev/null
+++ b/misc-scripts/xref_mapping/XrefMapper/sus_scrofa.pm
@@ -0,0 +1,82 @@
+package XrefMapper::sus_scrofa;
+
+use XrefMapper::BasicMapper;
+use XrefMapper::SubmitMapper;
+use strict;
+use vars '@ISA';
+
+@ISA = qw{ XrefMapper::BasicMapper };
+
+
+sub gene_description_filter_regexps {
+
+ return ('^BA\S+\s+\(NOVEL PROTEIN\)\.?',
+ '^DJ\S+\s+\(NOVEL PROTEIN\)\.?',
+ '^LOC\d+\s*(PROTEIN)?\.?',
+ '^Putative uncharacterized protein.*',
+ '^ORF.*',
+ '^PROTEIN C\d+ORF\d+\.*',
+ '\(CLONE \S+\)\s+',
+ '^BC\d+\_\d+\.?',
+ '^CGI\-\d+ PROTEIN\.?\;?',
+ '[0-9A-Z]{10}RIK PROTEIN[ \.]',
+ 'R\d{5}_\d[ \.,].*',
+ 'PROTEIN KIAA\d+[ \.].*',
+ 'RIKEN CDNA [0-9A-Z]{10}[ \.]',
+ '^\(*HYPOTHETICAL\s+.*',
+ '^UNKNOWN\s+.*',
+ '^DKFZP[A-Z0-9]+\s+PROTEIN[\.;]?.*',
+ '^CHROMOSOME\s+\d+\s+OPEN\s+READING\s+FRAME\s+\d+\.?.*',
+ '^FKSG\d+\.?.*',
+ '^HSPC\d+\s+PROTEIN\.?.*',
+ '^KIAA\d+\s+PROTEIN\.?.*',
+ '^KIAA\d+\s+GENE\s+PRODUCT\.?.*',
+ '^HSPC\d+.*',
+ '^PRO\d+\s+PROTEIN\.?.*',
+ '^PRO\d+\.?.*',
+ '^FLJ\d+\s+PROTEIN.*',
+ '^PRED\d+\s+PROTEIN.*',
+ '^WUGSC:.*\s+PROTEIN\.?.*',
+ '^SIMILAR TO GENE.*',
+ '^SIMILAR TO PUTATIVE[ \.]',
+ '^SIMILAR TO HYPOTHETICAL.*',
+ '^SIMILAR TO (KIAA|LOC).*',
+ '^SIMILAR TO\s+$',
+ '^WUGSC:H_.*',
+ '^\s*\(?PROTEIN\)?\.?\s*$',
+ '^\s*\(?FRAGMENT\)?\.?\s*$',
+ '^\s*\(?GENE\)?\.?\s*$',
+ '^\s*\(\s*\)\s*$',
+ '^\s*\(\d*\)\s*[ \.]$');
+
+}
+
+
+sub get_official_name{
+ return "PIGGY";
+}
+
+sub get_canonical_name{
+ return "PIGGY";
+}
+
+# Not running transcript_names_from_gene for merged species
+# as this is already beng done in the OfficialNaming mapper
+sub transcript_names_from_gene {
+ return;
+}
+
+
+# For merged species, display xref assigned from the stable_table
+# which has been populated by the OfficialNaming mapper
+sub set_display_xrefs{
+ my $self = shift;
+ my $display = XrefMapper::DisplayXrefs->new($self);
+ $display->set_display_xrefs_from_stable_table();
+
+}
+
+
+
+
+1;
--
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