From 14cec07a1da750e96db3a93944fef5c50fe61218 Mon Sep 17 00:00:00 2001
From: Arnaud Kerhornou <arnaud@ebi.ac.uk>
Date: Wed, 10 Aug 2011 13:33:14 +0000
Subject: [PATCH] Specific display_name and description assignment to pombe
---
.../XrefMapper/schizosaccharomyces_pombe.pm | 80 +++++++++++++++++++
1 file changed, 80 insertions(+)
create mode 100644 misc-scripts/xref_mapping/XrefMapper/schizosaccharomyces_pombe.pm
diff --git a/misc-scripts/xref_mapping/XrefMapper/schizosaccharomyces_pombe.pm b/misc-scripts/xref_mapping/XrefMapper/schizosaccharomyces_pombe.pm
new file mode 100644
index 0000000000..ca6d2aa57a
--- /dev/null
+++ b/misc-scripts/xref_mapping/XrefMapper/schizosaccharomyces_pombe.pm
@@ -0,0 +1,80 @@
+package XrefMapper::schizosaccharomyces_pombe;
+
+use XrefMapper::BasicMapper;
+
+use vars qw(@ISA);
+
+@ISA = qw(XrefMapper::BasicMapper);
+
+sub get_set_lists {
+
+ return [["ExonerateGappedBest1", ["schizosaccharomyces_pombe","*"]]];
+
+}
+
+
+
+# Pombe is imported from PomBase. The gene and transcript stable IDs
+# are the PomBase identifiers. The display_xref_ids for genes and
+# transcripts are calculated directly rather than via the more complex
+# priority-based method in BasicMapper.pm
+
+sub build_display_xrefs {
+
+ my ($self, $type, $external_db) = @_;
+
+ print "Setting $type display_xrefs from $type stable IDs\n";
+ my $dir = $self->core()->dir();
+
+ my $sql = "UPDATE $type t, ${type}_stable_id s, xref x, external_db e SET t.display_xref_id=x.xref_id WHERE t.${type}_id=s.${type}_id AND s.stable_id=x.dbprimary_acc AND e.external_db_id=x.external_db_id AND e.db_name=\'${external_db}\'\n";
+
+ open (SQL, ">$dir/${type}_display_xref.sql");
+
+ print SQL $sql;
+
+ close(SQL);
+
+}
+
+
+sub transcript_display_xref_sources {
+ my $self = shift;
+ my $fullmode = shift;
+
+ my @list = qw(
+ PomBase_GENE
+ PomBase_TRANSCRIPT
+ );
+
+ my %ignore;
+
+
+ # Both methods
+
+ if(!$fullmode){
+ $ignore{"EntrezGene"}= 'FROM:RefSeq_[pd][en][pa].*_predicted';
+ }
+ else{
+ $ignore{"EntrezGene"} = 'select ox.object_xref_id from object_xref ox, dependent_xref dx, source s1, xref x1, source s2, xref x2 where ox.object_xref_id = dx.object_xref_id and dx.dependent_xref_id = x1.xref_id and x1.source_id = s1.source_id and s1.name = "EntrezGene" and x2.xref_id = dx.master_xref_id and x2.source_id = s2.source_id and (s2.name like "Refseq_dna_predicted" or s2.name like "RefSeq_peptide_predicted") and ox.ox_status = "DUMP_OUT"';
+
+ }
+
+ return [\@list,\%ignore];
+}
+
+sub gene_description_sources {
+ return (
+ "PomBase_GENE"
+ );
+}
+
+
+sub gene_description_filter_regexps {
+
+ return ();
+
+}
+
+
+
+1;
--
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