From 6c3446c6ff3b58bdf83a0db86521c4877fa1f5a2 Mon Sep 17 00:00:00 2001
From: Ian Longden <ianl@sanger.ac.uk>
Date: Mon, 13 Dec 2010 13:19:21 +0000
Subject: [PATCH] Uniprot to all be done at 100 percent overlap.
---
.../xref_mapping/XrefMapper/homo_sapiens.pm | 38 ++++++++++++++++---
.../xref_mapping/XrefMapper/mus_musculus.pm | 17 ++++++++-
.../XrefMapper/rattus_norvegicus.pm | 10 ++---
3 files changed, 52 insertions(+), 13 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefMapper/homo_sapiens.pm b/misc-scripts/xref_mapping/XrefMapper/homo_sapiens.pm
index e780bad9b5..91a188c349 100644
--- a/misc-scripts/xref_mapping/XrefMapper/homo_sapiens.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/homo_sapiens.pm
@@ -7,20 +7,24 @@ use vars '@ISA';
@ISA = qw{ XrefMapper::BasicMapper };
-sub get_set_lists {
+# now uses the default settings.
+#sub get_set_lists {
+#
# return [["ExonerateGappedBest1", ["homo_sapiens","*"]]];
-
- return [["ExonerateGappedBest_100_perc_id", ["homo_sapiens","Uniprot/SWISSPROT"]],
- ["ExonerateGappedBest1", ["homo_sapiens","*" ]] ];
-
-}
+#
+# return [["ExonerateGappedBest_100_perc_id", ["homo_sapiens","Uniprot/SWISSPROT"]],
+# ["ExonerateGappedBest_100_perc_id", ["homo_sapiens","Uniprot/SPTREMBL"]],
+# ["ExonerateGappedBest1", ["homo_sapiens","*" ]] ];
+#
+#}
sub gene_description_filter_regexps {
return ('^BA\S+\s+\(NOVEL PROTEIN\)\.?',
'^DJ\S+\s+\(NOVEL PROTEIN\)\.?',
'^LOC\d+\s*(PROTEIN)?\.?',
+ '^Putative uncharacterized protein.*',
'^ORF.*',
'^PROTEIN C\d+ORF\d+\.*',
'\(CLONE \S+\)\s+',
@@ -93,6 +97,28 @@ JSQL
}
+#
+#for human display_xrefs and gene descriptions have already been set in official_naming
+#so we only beed to do the status's
+#
+#sub genes_and_transcripts_attributes_set{
+# my $self = shift;
+# print "NEED TO SET STATUS ONLY FOR HUMAN!!!\n";
+# $self->build_gene_transcript_status();
+#}
+
+sub set_display_xrefs{
+ my $self = shift;
+ my $display = XrefMapper::DisplayXrefs->new($self);
+ $display->set_display_xrefs_from_stable_table();
+
+}
+
+sub set_gene_descriptions(){
+ my $self = shift;
+ my $display = XrefMapper::DisplayXrefs->new($self);
+ $display->set_gene_descriptions_from_display_xref()
+}
# For human we want to make a copy of the HGNC references on the genes and put them on
# the "canonical" transcripts
diff --git a/misc-scripts/xref_mapping/XrefMapper/mus_musculus.pm b/misc-scripts/xref_mapping/XrefMapper/mus_musculus.pm
index a19076a374..9a761945fc 100644
--- a/misc-scripts/xref_mapping/XrefMapper/mus_musculus.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/mus_musculus.pm
@@ -7,10 +7,23 @@ use vars '@ISA';
@ISA = qw{ XrefMapper::BasicMapper };
use strict;
-sub get_set_lists {
+#sub get_set_lists {
+#
+# return [["ExonerateGappedBest1", ["mus_musculus","*"]]];
+#
+#}
- return [["ExonerateGappedBest1", ["mus_musculus","*"]]];
+sub set_display_xrefs{
+ my $self = shift;
+ my $display = XrefMapper::DisplayXrefs->new($self);
+ $display->set_display_xrefs_from_stable_table();
+
+}
+sub set_gene_descriptions(){
+ my $self = shift;
+ my $display = XrefMapper::DisplayXrefs->new($self);
+ $display->set_gene_descriptions_from_display_xref()
}
sub get_official_name{
diff --git a/misc-scripts/xref_mapping/XrefMapper/rattus_norvegicus.pm b/misc-scripts/xref_mapping/XrefMapper/rattus_norvegicus.pm
index 6373e5cbdc..58c381d5d7 100644
--- a/misc-scripts/xref_mapping/XrefMapper/rattus_norvegicus.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/rattus_norvegicus.pm
@@ -6,11 +6,11 @@ use vars '@ISA';
@ISA = qw{ XrefMapper::BasicMapper };
-sub get_set_lists {
-
- return [["ExonerateGappedBest1", ["rattus_norvegicus","*"]]];
-
-}
+#sub get_set_lists {
+#
+# return [["ExonerateGappedBest1", ["rattus_norvegicus","*"]]];
+#
+#}
--
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