species.pm for pig

misc-scripts/xref_mapping/XrefMapper/sus_scrofa.pm

+package XrefMapper::sus_scrofa;
+
+use  XrefMapper::BasicMapper;
+
+use vars '@ISA';
+
+@ISA = qw{ XrefMapper::BasicMapper };
+
+sub get_set_lists{
+
+  return [["ExonerateGappedBest5", ["xenopus_tropicalis","RefSeq_mRNA"]],
+	  ["ExonerateGappedBest5", ["xenopus_tropicalis","RefSeq_mRNA_predicted"]],
+	  ["ExonerateGappedBest5", ["xenopus_tropicalis","RefSeq_ncRNA"]],
+	  ["ExonerateGappedBest5", ["xenopus_tropicalis","RefSeq_ncRNA_predicted"]],
+          ["ExonerateGappedBest1", ["xenopus_tropicalis","*"]]];
+
+}
+
+sub gene_description_filter_regexps {
+
+  return ('^UNKNOWN\s+.*',
+          '^undefined.*');
+
+}
+
+
+
+sub transcript_display_xref_sources {
+  my $self     = shift;
+
+  my @list = qw(HGNC
+                MGI
+                Clone_based_vega_gene
+                Clone_based_ensembl_gene
+                HGNC_transcript_name
+                MGI_transcript_name
+                Clone_based_vega_transcript
+                Clone_based_ensembl_transcript
+                miRBase
+                RFAM
+                IMGT/GENE_DB
+                SGD
+                flybase_symbol
+                Anopheles_symbol
+                Genoscope_annotated_gene
+                Uniprot_genename
+                Uniprot/SWISSPROT
+                Uniprot/Varsplic
+                Uniprot/SPTREMBL
+                EntrezGene
+                RefSeq_mRNA
+                RefSeq_ncRNA
+                RefSeq_dna
+                RefSeq_peptide);
+
+  my %ignore;
+
+  $ignore{"EntrezGene"} =(<<'IEG');
+SELECT DISTINCT ox.object_xref_id
+  FROM object_xref ox, dependent_xref dx, 
+       xref xmas, xref xdep, 
+       source smas, source sdep
+    WHERE ox.xref_id = dx.dependent_xref_id AND
+          dx.dependent_xref_id = xdep.xref_id AND
+          dx.master_xref_id = xmas.xref_id AND
+          xmas.source_id = smas.source_id AND
+          xdep.source_id = sdep.source_id AND
+          smas.name like "Refseq%predicted" AND
+          sdep.name like "EntrezGene" AND
+          ox.ox_status = "DUMP_OUT"
+IEG
+
+  $ignore{"Uniprot/SPTREMBL"} =(<<BIGN);
+SELECT object_xref_id
+    FROM object_xref JOIN xref USING(xref_id) JOIN source USING(source_id)
+     WHERE ox_status = 'DUMP_OUT' AND name = 'Uniprot/SPTREMBL' 
+      AND priority_description = 'protein_evidence_gt_2'
+BIGN
+
+
+  return [\@list,\%ignore];
+}
+
+1;