From 34cb21ea6ffc5205d3d457a9fa453c159622096b Mon Sep 17 00:00:00 2001
From: Karyn Megy <kmegy@sanger.ac.uk>
Date: Fri, 29 May 2009 15:54:10 +0000
Subject: [PATCH] For running Culex Xrefs
---
.../Methods/ExonerateGappedBest1_culex.pm | 26 +++++++++
.../xref_mapping/XrefMapper/culex_pipiens.pm | 54 +++++++++++++++++++
2 files changed, 80 insertions(+)
create mode 100644 misc-scripts/xref_mapping/XrefMapper/Methods/ExonerateGappedBest1_culex.pm
create mode 100644 misc-scripts/xref_mapping/XrefMapper/culex_pipiens.pm
diff --git a/misc-scripts/xref_mapping/XrefMapper/Methods/ExonerateGappedBest1_culex.pm b/misc-scripts/xref_mapping/XrefMapper/Methods/ExonerateGappedBest1_culex.pm
new file mode 100644
index 0000000000..544371a697
--- /dev/null
+++ b/misc-scripts/xref_mapping/XrefMapper/Methods/ExonerateGappedBest1_culex.pm
@@ -0,0 +1,26 @@
+package XrefMapper::Methods::ExonerateGappedBest1_culex;
+
+use XrefMapper::Methods::ExonerateBasic;
+
+use vars '@ISA';
+
+@ISA = qw{XrefMapper::Methods::ExonerateBasic};
+
+
+
+sub options {
+
+ return ('--gappedextension FALSE', '--model', 'affine:local', '--subopt', 'no', '--bestn', '1');
+
+}
+
+sub query_identity_threshold {
+ return 55;
+}
+
+sub target_identity_threshold {
+ return 55;
+}
+
+
+1;
diff --git a/misc-scripts/xref_mapping/XrefMapper/culex_pipiens.pm b/misc-scripts/xref_mapping/XrefMapper/culex_pipiens.pm
new file mode 100644
index 0000000000..7308271f0e
--- /dev/null
+++ b/misc-scripts/xref_mapping/XrefMapper/culex_pipiens.pm
@@ -0,0 +1,54 @@
+
+package XrefMapper::culex_pipiens;
+
+use XrefMapper::BasicMapper;
+use XrefMapper::VBCoordinateMapper;
+
+use vars '@ISA';
+
+@ISA = qw{ XrefMapper::BasicMapper };
+
+sub get_set_lists {
+
+ return [["ExonerateGappedBest1_culex", ["culex_pipiens","*"]]];
+
+}
+
+# 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;
+ return [\@list,\%ignore];
+
+}
+
+# regexps to match any descriptons we want to filter out
+sub gene_description_filter_regexps {
+
+ return ();
+
+}
+
+1;
--
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