diff --git a/misc-scripts/xref_mapping/XrefMapper/danio_rerio.pm b/misc-scripts/xref_mapping/XrefMapper/danio_rerio.pm index 115b242f4223602cb6b90a9dfcb591a1c753bbda..3e051655b5dc70c54abe7140f9c43f742e237381 100644 --- a/misc-scripts/xref_mapping/XrefMapper/danio_rerio.pm +++ b/misc-scripts/xref_mapping/XrefMapper/danio_rerio.pm @@ -92,16 +92,24 @@ sub transcript_display_xref_sources { my %ignore; - $ignore{"EntrezGene"} =(<<AIGN); - -SELECT ox.object_xref_id - FROM object_xref ox, dependent_xref dx, source s1, xref x1, source s2, xref x2 - WHERE ox.object_xref_id = dx.object_xref_id AND dx.dependent_xref_id = x1.xref_id - AND x1.source_id = s1.source_id and s1.name = 'EntrezGene' - AND x2.xref_id = dx.master_xref_id and x2.source_id = s2.source_id - AND (s2.name like 'Refseq_dna_predicted' or s2.name like 'RefSeq_peptide_predicted') - AND ox.ox_status = 'DUMP_OUT' -AIGN + if(!$fullmode){ + $ignore{"EntrezGene"}= 'FROM:RefSeq_[pd][en][pa].*_predicted'; + } + else{ + $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 @@ -109,6 +117,8 @@ SELECT object_xref_id WHERE ox_status = 'DUMP_OUT' AND name = 'Uniprot/SPTREMBL' AND priority_description = 'protein_evidence_gt_3' BIGN + + } return [\@list,\%ignore];