diff --git a/misc-scripts/xref_mapping/XrefMapper/DisplayXrefs.pm b/misc-scripts/xref_mapping/XrefMapper/DisplayXrefs.pm index 7cf207992a27a2fcda9d6764f70390eb208a47ed..4cb3b6b87df7bae5c246107de8bd76deabe3ac1d 100644 --- a/misc-scripts/xref_mapping/XrefMapper/DisplayXrefs.pm +++ b/misc-scripts/xref_mapping/XrefMapper/DisplayXrefs.pm @@ -78,11 +78,26 @@ sub transcript_display_xref_sources { $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"'; + $ignore{"EntrezGene"} =(<<AIGN); + +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' +AIGN + + $ignore{"Uniprot/SPTREMBL"} =(<<BIGN); +SELECT object_xref_id + FROM object_xref JOIN xref USING(xref_id) JOIN source USING(source_id) + WHERE ox_status = 'DUMP_OUT' AND name = 'Uniprot/SPTREMBL' + AND priority_description = 'protein_evidence_gt_3' +BIGN } - return [\@list,\%ignore]; } @@ -459,8 +474,6 @@ sub build_transcript_and_gene_display_xrefs { print "Building Transcript and Gene display_xrefs Using OLD methods accessing core database alone.\n" if ($self->verbose); - - my %external_name_to_id; my $sql1 = "SELECT external_db_id, db_name, status from external_db"; @@ -1266,6 +1279,8 @@ sub set_display_xrefs{ my $update_gene_sth = $self->core->dbc->prepare("UPDATE gene g SET g.display_xref_id= ? WHERE g.gene_id=?"); my $update_tran_sth = $self->core->dbc->prepare("UPDATE transcript t SET t.display_xref_id= ? WHERE t.transcript_id=?"); + #get hash for sources in hash + #get priority description my $sql =(<<SQL); CREATE TABLE display_xref_prioritys(