Commit 6c3446c6 authored by Ian Longden's avatar Ian Longden
Browse files

Uniprot to all be done at 100 percent overlap.

parent c722db73
......@@ -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
......
......@@ -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{
......
......@@ -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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