From 58422e42ecd6d85b4970befdb520b1562e2b7622 Mon Sep 17 00:00:00 2001
From: Glenn Proctor <gp1@sanger.ac.uk>
Date: Fri, 12 Nov 2004 10:25:51 +0000
Subject: [PATCH] Changed Uniprot source names.
---
misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm | 12 ++++++------
.../xref_mapping/XrefParser/UniProtParser.pm | 4 ++--
2 files changed, 8 insertions(+), 8 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm b/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
index 65b95cd414..61ab32ac03 100644
--- a/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
@@ -149,11 +149,11 @@ sub get_species_id_from_species_name{
sub get_set_lists{
my ($self) = @_;
-# return [["method1",["homo_sapiens","RefSeq"],["homo_sapiens","UniProtSwissProt"]],
+# return [["method1",["homo_sapiens","RefSeq"],["homo_sapiens","Uniprot/SWISSPROT"]],
# ["method2",[$self->species,"*"]],
# ["method3",["*","*"]]];
- #return [["ExonerateGappedBest1", ["homo_sapiens","UniProtSwissProt"]]];
+ #return [["ExonerateGappedBest1", ["homo_sapiens","Uniprot/SWISSPROT"]]];
return [["ExonerateGappedBest1", ["homo_sapiens","RefSeq"]]];
# return [["ExonerateBest1",["*","*"]]];
@@ -952,7 +952,7 @@ sub dump_xrefs {
$dep_sth->bind_columns(\$xref_id, \$accession, \$label, \$description, \$source_id);
while (my @row = $dep_sth->fetchrow_array()) {
- print XREF ($xref_id+$xref_id_offset) . "\t" . $accession . "\t" . $label . "\t" . $description . "DEPENDENT\n";
+ print XREF ($xref_id+$xref_id_offset) . "\t" . $accession . "\t" . $label . "\t" . $description . "\tDEPENDENT\n";
$source_ids{$source_id} = $source_id;
# create an object_xref linking this (dependent) xref with any objects it maps to
@@ -962,7 +962,7 @@ sub dump_xrefs {
print "xref $accession has " . scalar(@objects) . " associated ensembl objects\n";
foreach my $object_id (@objects) {
my $type = $ensembl_object_types{$object_id};
- print OBJECT_XREF "$object_xref_id\t$object_id\t$type\t" . ($xref_id+$xref_id_offset) . "DEPENDENT\n";
+ print OBJECT_XREF "$object_xref_id\t$object_id\t$type\t" . ($xref_id+$xref_id_offset) . "\tDEPENDENT\n";
$object_xref_id++;
# Add this mapping to the list - note NON-OFFSET xref_id is used
my $key = $type . ":" . $object_id;
@@ -1155,9 +1155,9 @@ sub transcript_display_xref_sources {
'Genoscope_annotated_gene',
'Genoscope_predicted_transcript',
'Genoscope_predicted_gene',
- 'UniProtSwissProt',
+ 'Uniprot/SWISSPROT',
'RefSeq',
- 'UniProtSPTrEMBL',
+ 'Uniprot/SPTREMBL',
'LocusLink');
}
diff --git a/misc-scripts/xref_mapping/XrefParser/UniProtParser.pm b/misc-scripts/xref_mapping/XrefParser/UniProtParser.pm
index 3fd560e24a..1aca898d0a 100644
--- a/misc-scripts/xref_mapping/XrefParser/UniProtParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/UniProtParser.pm
@@ -42,8 +42,8 @@ sub run {
my ($species_id, $species_name) = get_species($file);
- $sp_source_id = XrefParser::BaseParser->get_source_id_for_source_name('UniProtSwissProt');
- $sptr_source_id = XrefParser::BaseParser->get_source_id_for_source_name('UniProtSPTrEMBL');
+ $sp_source_id = XrefParser::BaseParser->get_source_id_for_source_name('Uniprot/SWISSPROT');
+ $sptr_source_id = XrefParser::BaseParser->get_source_id_for_source_name('Uniprot/SPTREMBL');
print "SwissProt source id for $file: $sp_source_id\n";
print "SpTREMBL source id for $file: $sptr_source_id\n";
--
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