From 02aa20b4f18b8b1e31b9d13ea7a6f9e33e54b7a1 Mon Sep 17 00:00:00 2001
From: Glenn Proctor <gp1@sanger.ac.uk>
Date: Wed, 21 Sep 2005 13:46:45 +0000
Subject: [PATCH] Formatting.
---
misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm | 12 +++++++++---
1 file changed, 9 insertions(+), 3 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm b/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
index ea4350e004..4debaf2ac3 100644
--- a/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
@@ -700,6 +700,7 @@ sub run_mapping {
$method_query_threshold{$method} = $obj->query_identity_threshold();
$method_target_threshold{$method} = $obj->target_identity_threshold();
+
if (!defined($self->use_existing_mappings)) {
my $job_name = $obj->run($queryfile, $targetfile, $self->core->dir());
push @job_names, $job_name;
@@ -710,8 +711,10 @@ sub run_mapping {
} # foreach method
+
if (!defined($self->use_existing_mappings)) {
# submit depend job to wait for all mapping jobs
+
submit_depend_job($self->core->dir, @job_names);
}
$self->check_err($self->core->dir);
@@ -2032,8 +2035,6 @@ sub map_source_to_external_db {
sub cleanup_sources_file{
my ($self,$id) = @_;
-
-
$updated_source{$id} =1;
my $dir = $self->core->dir();
@@ -2547,7 +2548,12 @@ sub compare_xref_descriptions {
sub gene_description_sources {
- return ("RefSeq_dna_predicted", "RefSeq_peptide_predicted", "Uniprot/SPTREMBL", "RefSeq_dna", "RefSeq_peptide", "Uniprot/SWISSPROT");
+ return ("RefSeq_dna_predicted",
+ "RefSeq_peptide_predicted",
+ "Uniprot/SPTREMBL",
+ "RefSeq_dna",
+ "RefSeq_peptide",
+ "Uniprot/SWISSPROT");
}
--
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