From 2b71caff6c4191d66638cbc0d5d9cd3d4dc5cc8b Mon Sep 17 00:00:00 2001
From: Ian Longden <ianl@sanger.ac.uk>
Date: Wed, 18 Mar 2009 14:46:57 +0000
Subject: [PATCH] verbose changes
---
misc-scripts/xref_mapping/XrefMapper/CoreInfo.pm | 7 ++++---
misc-scripts/xref_mapping/XrefMapper/Interpro.pm | 11 ++++++-----
.../xref_mapping/XrefMapper/ProcessPrioritys.pm | 5 +++--
3 files changed, 13 insertions(+), 10 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefMapper/CoreInfo.pm b/misc-scripts/xref_mapping/XrefMapper/CoreInfo.pm
index 0788628cf7..c81a9d1e93 100644
--- a/misc-scripts/xref_mapping/XrefMapper/CoreInfo.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/CoreInfo.pm
@@ -37,6 +37,7 @@ sub new {
bless $self,$class;
$self->core($mapper->core);
$self->xref($mapper->xref);
+ $self->verbose($mapper->verbose);
return $self;
}
@@ -131,7 +132,7 @@ SQL
$internal_id = $stable_id;
}
else{
- print "Could not find stable id $stable_id in table to get the internal id hence ignoring!!!\n" if($self->mapper->verbose);
+ print "Could not find stable id $stable_id in table to get the internal id hence ignoring!!!\n" if($self->verbose);
$err_count++;
next;
}
@@ -176,9 +177,9 @@ SQL
}
$sth->finish;
if($duplicate_direct_count or $duplicate_dependent_count){
- print "duplicate entrys ignored for $duplicate_direct_count direct xrefs and $duplicate_dependent_count dependent xrefs\n" if($self->mapper->verbose);
+ print "duplicate entrys ignored for $duplicate_direct_count direct xrefs and $duplicate_dependent_count dependent xrefs\n" if($self->verbose);
}
- if($err_count or $self->mapper->verbose){
+ if($err_count or $self->verbose){
print STDERR $count." direct_xrefs added to ensembl ".$table."s BUT $err_count stable ids could not be found\n";
}
}
diff --git a/misc-scripts/xref_mapping/XrefMapper/Interpro.pm b/misc-scripts/xref_mapping/XrefMapper/Interpro.pm
index 4dd8ce76bc..4c1819007e 100644
--- a/misc-scripts/xref_mapping/XrefMapper/Interpro.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/Interpro.pm
@@ -14,6 +14,7 @@ sub new {
bless $self,$class;
$self->core($mapper->core);
$self->xref($mapper->xref);
+ $self->verbose($mapper->verbose);
return $self;
}
@@ -21,7 +22,7 @@ sub new {
sub process{
my $self = shift;
- print "Writing InterPro\n" if($self->mapper->verbose);
+ print "Writing InterPro\n" if($self->verbose);
my( $ipro_count, $xref_count, $oxref_count, $goxref_count ) = (0,0,0,0);
my $object_xref_id;
@@ -93,11 +94,11 @@ sub process{
$sth->finish();
- print "\n".$dup." already existed\n\n" if($self->mapper->verbose);
+ print "\n".$dup." already existed\n\n" if($self->verbose);
- print(" Wrote $ipro_count interpro table entries\n") if($self->mapper->verbose);
- print(" including $oxref_count object xrefs, \n") if($self->mapper->verbose);
- print(" and $goxref_count go xrefs\n") if($self->mapper->verbose);
+ print(" Wrote $ipro_count interpro table entries\n") if($self->verbose);
+ print(" including $oxref_count object xrefs, \n") if($self->verbose);
+ print(" and $goxref_count go xrefs\n") if($self->verbose);
# foreach my $key (keys %added){
# print "id= $key has ".$added{$key}. " object xrefs added\n";
# }
diff --git a/misc-scripts/xref_mapping/XrefMapper/ProcessPrioritys.pm b/misc-scripts/xref_mapping/XrefMapper/ProcessPrioritys.pm
index 6cabf6d096..3ffaa47638 100644
--- a/misc-scripts/xref_mapping/XrefMapper/ProcessPrioritys.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/ProcessPrioritys.pm
@@ -32,6 +32,7 @@ sub new {
bless $self,$class;
# $self->core($mapper->core);
$self->xref($mapper->xref);
+ $self->verbose($mapper->verbose);
return $self;
}
@@ -65,9 +66,9 @@ sub process {
my @names = $self->get_priority_names();
- print "The foillowing will be processed as priority xrefs\n" if($self->mapper->verbose);
+ print "The foillowing will be processed as priority xrefs\n" if($self->verbose);
foreach my $name (@names){
- print "\t$name\n" if($self->mapper->verbose);
+ print "\t$name\n" if($self->verbose);
}
my $update_ox_sth = $self->xref->dbc->prepare('update object_xref set ox_status = "FAILED_PRIORITY" where object_xref_id = ?');
--
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