From 469e7c0f4d6fb0cee50fdabcfae10f9ab95b3cb8 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andreas=20Kusalananda=20K=C3=A4h=C3=A4ri?=
<ak4@sanger.ac.uk>
Date: Tue, 13 Mar 2007 14:36:34 +0000
Subject: [PATCH] Get rid of warnings.
---
.../xref_mapping/XrefMapper/BasicMapper.pm | 25 ++++++++-----------
1 file changed, 11 insertions(+), 14 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm b/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
index eab16889af..2d41e7fe17 100644
--- a/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
@@ -1396,7 +1396,7 @@ PSQL
print STDERR "no extra bit for $acc ($xref_id)\n";
print XREF_P "\n";
}
- $xrefs_written{$xref_id};
+ $xrefs_written{$xref_id} = 1;
$priority_seenit{$key} = "SEEN_IT";
}
$sth->finish;
@@ -2939,7 +2939,7 @@ GADES
$sth->execute();
- my $sth = $core_db->prepare(<<TRAN);
+ $sth = $core_db->prepare(<<TRAN);
UPDATE transcript t
SET t.display_xref_id=NULL
TRAN
@@ -2947,7 +2947,7 @@ TRAN
$sth->execute();
# gene descriptions
- my $sth = $core_db->prepare(<<GENE);
+ $sth = $core_db->prepare(<<GENE);
UPDATE gene g
SET g.description=NULL
GENE
@@ -2979,7 +2979,7 @@ GENE
print FILE "INSERT INTO meta (meta_key,meta_value) VALUES ('xref.timestamp', NOW())\n";
close(FILE);
- my $mysql_command = $self->get_mysql_command($core_db);
+ $mysql_command = $self->get_mysql_command($core_db);
system( "$mysql_command < $file" ) == 0
or print( "ERROR: parsing $file in mysql\n" );
@@ -3007,7 +3007,7 @@ GENE
print FILE "AND x.external_db_id = e.external_db_id AND e.status=\'KNOWNXREF\';\n";
close(FILE);
- my $mysql_command = $self->get_mysql_command($core_db);
+ $mysql_command = $self->get_mysql_command($core_db);
system( "$mysql_command < $file" ) == 0
or print( "ERROR: parsing $file in mysql\n" );
}
@@ -3759,7 +3759,7 @@ EOS
print STDERR "PROBLEM: key =$key\n\txref = $xref_id\n\toffset is $xref_id_offset\n";
}
print XREF2 "\tINFERRED_PAIR\tGenerated via its Pair ".$priority_seenit{$key}."\n";
- $xrefs_written{$xref_id};
+ $xrefs_written{$xref_id} = 1;
}
$sth->finish;
@@ -3826,7 +3826,7 @@ EOS
print XREF2 ($xref_id+$xref_id_offset)."\t". $source_to_external_db{$source_id}.
"\t$acc\t$label\t$ver\t$desc";
print XREF2 "\tDEPENDENT\tGenerated via ".$master_acc{$good2missed{$goodxref}-$xref_id_offset}."\n";
- $xrefs_written{$xref_id};
+ $xrefs_written{$xref_id} = 1;
}
$max_object_xref_id++;
@@ -3860,7 +3860,7 @@ EOS
print XREF2 ($xref_id+$xref_id_offset)."\t". $source_to_external_db{$source_id}.
"\t$acc\t$label\t$ver\t$desc";
print XREF2 "\tDEPENDENT\tGenerated via ".$master_acc{$good2missed{$goodxref}-$xref_id_offset}."\n";
- $xrefs_written{$xref_id};
+ $xrefs_written{$xref_id} = 1;
}
$max_object_xref_id++;
@@ -3911,7 +3911,7 @@ EOS
print XREF2 ($xref_id+$xref_id_offset)."\t". $source_to_external_db{$source_id}.
"\t$acc\t$label\t$ver\t$desc";
print XREF2 "\tDEPENDENT\tGenerated via ".$master_acc{$good2missed{$goodxref}-$xref_id_offset}."\n";
- $xrefs_written{$xref_id};
+ $xrefs_written{$xref_id} = 1;
}
@@ -3946,7 +3946,7 @@ EOS
print XREF2 ($xref_id+$xref_id_offset)."\t". $source_to_external_db{$source_id}.
"\t$acc\t$label\t$ver\t$desc";
print XREF2 "\tDEPENDENT\tGenerated via ".$master_acc{$good2missed{$goodxref}-$xref_id_offset}."\n";
- $xrefs_written{$xref_id};
+ $xrefs_written{$xref_id} = 1;
}
$max_object_xref_id++;
@@ -3985,7 +3985,7 @@ EOS
print "$added_transcript transcripts\n";
}
- my $file = $self->core->dir()."/pairs_xref.txt";
+ $file = $self->core->dir()."/pairs_xref.txt";
if(-s $file){
my $sth = $self->core->dbc->prepare("LOAD DATA LOCAL INFILE \'$file\' IGNORE INTO TABLE xref");
@@ -4205,8 +4205,6 @@ sub unmapped_data_for_prioritys{
# else if priotrity_failed
#write unmapped object.
- my $description_missed = "Unable to match to any ensembl entity at all";
-
my $sth = $self->core->dbc->prepare("select unmapped_reason_id from unmapped_reason where full_description like '".$description_missed."'");
$sth->execute();
my $xref_missed_id;
@@ -4381,7 +4379,6 @@ sub write_dependent_unmapped_objects{
}
$sth->finish;
- my $max_unmapped_object_id;
$sth = $self->core->dbc->prepare("select MAX(unmapped_object_id) ".
"from unmapped_object");
$sth->execute();
--
GitLab