From fc77a81a2cfadd773484b6ca39f2662e608c3b8a Mon Sep 17 00:00:00 2001
From: Monika Komorowska <mk8@sanger.ac.uk>
Date: Thu, 22 Mar 2012 14:05:17 +0000
Subject: [PATCH] species.pm for pig
---
.../xref_mapping/XrefMapper/sus_scrofa.pm | 84 +++++++++++++++++++
1 file changed, 84 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..7e41d47aa5
--- /dev/null
+++ b/misc-scripts/xref_mapping/XrefMapper/sus_scrofa.pm
@@ -0,0 +1,84 @@
+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;
--
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