From 17205473c6c67812e0cee7b1ba92b3b1fc05d8c8 Mon Sep 17 00:00:00 2001
From: Monika Komorowska <mk8@sanger.ac.uk>
Date: Mon, 9 Jan 2012 15:02:24 +0000
Subject: [PATCH] load core data before mapping stage
---
misc-scripts/xref_mapping/xref_mapper.pl | 23 +++++++++--------------
1 file changed, 9 insertions(+), 14 deletions(-)
diff --git a/misc-scripts/xref_mapping/xref_mapper.pl b/misc-scripts/xref_mapping/xref_mapper.pl
index 443fc967e7..48034c14ee 100644
--- a/misc-scripts/xref_mapping/xref_mapper.pl
+++ b/misc-scripts/xref_mapping/xref_mapper.pl
@@ -87,7 +87,8 @@ my $mapper = XrefMapper::BasicMapper->process_file($file, !$notverbose, $no_xref
if(defined($recalc_display_xrefs)){
- $mapper->official_naming();
+ my $official_naming = XrefMapper::OfficialNaming->new($mapper);
+ $official_naming->run();
my $display = XrefMapper::DisplayXrefs->new($mapper);
# $display->set_display_xrefs_from_stable_table();
$display->genes_and_transcripts_attributes_set($no_xref);
@@ -149,17 +150,17 @@ else{
$submitter->no_dump_xref()
}
-
+$status = $mapper->xref_latest_status();
+if($status eq "core_fasta_dumped"){# load core data needed
+ my $core_info = XrefMapper::CoreInfo->new($mapper);
+ $core_info->get_core_data();
+}
$status = $mapper->xref_latest_status();
-if($status eq "core_fasta_dumped"){
+if($status eq "core_data_loaded") {
$submitter->build_list_and_map();
$status = $mapper->xref_latest_status();
}
-else{
-
-}
-
$status = $mapper->xref_latest_status();
if($status eq "mapping_started"){
@@ -171,13 +172,7 @@ elsif($status eq "mapping_finished"){
}
$status = $mapper->xref_latest_status();
-if($status eq "mapping_processed"){ # load core data needed
- my $core_info = XrefMapper::CoreInfo->new($mapper);
- $core_info->get_core_data();
-}
-
-$status = $mapper->xref_latest_status();
-if($status eq "core_data_loaded"){ # add direct xrefs to the object_xref etctables
+if($status eq "mapping_processed"){ # add direct xrefs to the object_xref etctables
my $direct_mappings = XrefMapper::DirectXrefs->new($mapper);
$direct_mappings->process();
}
--
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