From ad2b05160fa196efc98871a5b680f68402e6b910 Mon Sep 17 00:00:00 2001
From: Monika Komorowska <mk8@sanger.ac.uk>
Date: Thu, 3 May 2012 16:39:23 +0000
Subject: [PATCH] replaced with culex_quinquefasciatus.pm
---
.../xref_mapping/XrefMapper/culex_pipiens.pm | 65 -------------------
1 file changed, 65 deletions(-)
delete mode 100644 misc-scripts/xref_mapping/XrefMapper/culex_pipiens.pm
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 7fa7659adb..0000000000
--- 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;
--
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