diff --git a/misc-scripts/xref_mapping/XrefMapper/tetraodon_nigroviridis.pm b/misc-scripts/xref_mapping/XrefMapper/tetraodon_nigroviridis.pm index 74c9cf8073a488f331bec5293bf4e7277605ea36..398adf8e359923b31373db824a6ee08ea17e3b5e 100644 --- a/misc-scripts/xref_mapping/XrefMapper/tetraodon_nigroviridis.pm +++ b/misc-scripts/xref_mapping/XrefMapper/tetraodon_nigroviridis.pm @@ -6,34 +6,62 @@ use vars '@ISA'; @ISA = qw{ XrefMapper::BasicMapper }; -# Same as in BasicMapper but Genoscope order reversed. +sub gene_display_xref_sources { + my $self = shift; + + my @list = qw(Genoscope_annotated_gene + RFAM + miRBase + Uniprot_genename + EntrezGene + Genoscope_pred_gene +); -sub transcript_display_xref_sources { + my %ignore; - my @list = qw(HGNC - MGI - wormbase_transcript - flybase_symbol - Anopheles_symbol - Genoscope_annotated_gene - Genoscope_predicted_transcript - Uniprot/SWISSPROT - RefSeq - Uniprot/SPTREMBL - LocusLink); + #don't use EntrezGene labels dependent on predicted RefSeqs - my %ignore; +$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 - $ignore{"Uniprot/SPTREMBL"} =(<<BIGN); -SELECT object_xref_id - FROM object_xref JOIN xref USING(xref_id) JOIN source USING(source_id) - WHERE ox_status = 'DUMP_OUT' AND name = 'Uniprot/SPTREMBL' - AND priority_description = 'protein_evidence_gt_2' -BIGN + #don't use labels starting with LOC +$ignore{'LOC_prefix'} =<<LOCP; +SELECT object_xref_id + FROM object_xref JOIN xref USING(xref_id) JOIN source USING(source_id) + WHERE ox_status = 'DUMP_OUT' AND label REGEXP '^LOC[[:digit:]]+' +LOCP return [\@list,\%ignore]; +} + +sub transcript_display_xref_sources { + + my @list = qw( + Genoscope_ann_transcript + RFAM + miRBase + Uniprot/SWISSPROT + Uniprot/Varsplic + Genoscope_pred_transcript +); + + my %ignore; + + return [\@list,\%ignore]; }