diff --git a/misc-scripts/xref_mapping/XrefMapper/culex_pipiens.pm b/misc-scripts/xref_mapping/XrefMapper/culex_pipiens.pm deleted file mode 100644 index 7fa7659adb1f60c43209dbd663f7871600e340fb..0000000000000000000000000000000000000000 --- a/misc-scripts/xref_mapping/XrefMapper/culex_pipiens.pm +++ /dev/null @@ -1,65 +0,0 @@ -package XrefMapper::culex_pipiens; - -use XrefMapper::BasicMapper; -use XrefMapper::VBCoordinateMapper; - -use vars '@ISA'; - -@ISA = qw{ XrefMapper::BasicMapper }; - -sub set_methods{ - - my $default_method = 'ExonerateGappedBest1_55_perc_id'; - my %override_method_for_source = ( - ExonerateGappedBest5_55_perc_id => ['RefSeq_mRNA','RefSeq_mRNA_predicted', 'RefSeq_ncRNA', 'RefSeq_ncRNA_predicted' ], - ); - - return $default_method, \%override_method_for_source; -} - -# transcript, gene display_xrefs can use defaults -# since anopheles_symbol is "before" Uniprot - -# If there is an Anopheles_symbol xref, use its description -sub gene_description_sources { - - return ("Anopheles_symbol", - "Uniprot/SWISSPROT", - "RefSeq_peptide", - "RefSeq_dna", - "Uniprot/SPTREMBL", - #"RefSeq_peptide_predicted", - #"RefSeq_dna_predicted", - #"EntrezGene"); - ); -} - -sub transcript_display_xref_sources { - - my @list = qw(RFAM - miRBase - Uniprot/SWISSPROT - Uniprot/Varsplic - Uniprot/SPTREMBL); - - my %ignore; - - $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]; - -} - -# regexps to match any descriptons we want to filter out -sub gene_description_filter_regexps { - - return (); - -} - -1;