From 7a0b7d564669f1d3d25084078b53a8e482f37e12 Mon Sep 17 00:00:00 2001
From: Ian Longden <ianl@sanger.ac.uk>
Date: Tue, 6 Feb 2007 13:27:34 +0000
Subject: [PATCH] delte unmapped object where the type is xref now done
automatically
---
misc-scripts/xref_mapping/xref_mapper.pl | 13 -------------
1 file changed, 13 deletions(-)
diff --git a/misc-scripts/xref_mapping/xref_mapper.pl b/misc-scripts/xref_mapping/xref_mapper.pl
index d0bbaa2da9..a73f4a23ae 100644
--- a/misc-scripts/xref_mapping/xref_mapper.pl
+++ b/misc-scripts/xref_mapping/xref_mapper.pl
@@ -20,7 +20,6 @@ xref_mapper.pl - Create Ensembl gene model xref mappings
[B<-upload>]
[B<-delete_external_db>]
[B<-notriage>]
-[B<-delete_unmapped>]
[B<-recalc_display_xrefs>}
[B<-dumpcheck>]
[B<-external_db_file>]
@@ -100,10 +99,6 @@ should be displayed.
don't dump triage data
-=item B<-delete_unmapped>
-
-deletes data from the unmapped_object table.
-
=item B<EXAMPLE:>
perl xref_mapper.pl -file mapper.input
@@ -157,7 +152,6 @@ my $delete_external_db ;
my $location;
my $logic_name;
my $notriage=undef;
-my $delete_unmapped = undef;
my $recalc_display_xrefs = undef;
my $external_db_file="/../external_db/external_dbs.txt";
@@ -171,7 +165,6 @@ GetOptions ('file=s' => \$file,
'location=s' => \$location,
'logicname=s' => \$logic_name,
'notriage' => \$notriage,
- 'delete_unmapped' => \$delete_unmapped,
'recalc_display_xrefs_only' => \$recalc_display_xrefs,
'external_db_file=s' => \$external_db_file,
'help' => \$help,
@@ -347,16 +340,12 @@ else{
$mapper->xref($xref); # attach xref object to mapper object
-#testing remove after
-
-
if(defined($recalc_display_xrefs)){
$mapper->genes_and_transcripts_attributes_set();
print "Finished recalculating display xrefs and gene descriptions";
exit;
}
-
print "\nDumping xref & Ensembl sequences\n";
$mapper->dump_seqs($location);
@@ -375,11 +364,9 @@ $mapper->parse_mappings($notriage);
if($upload){
- $mapper->delete_unmapped() if ($delete_unmapped);
$mapper->do_upload();
-
print "\nProcessing priority xrefs\n";
$mapper->process_priority_xrefs();
--
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