diff --git a/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm b/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
index 8924300dbe13d7cd147ea2dbcdea319c81e13987..c1c25cd433c10c0f5ed51419a6a1c16b53c5da2e 100644
--- a/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
@@ -856,6 +856,7 @@ sub parse_mappings {
} else {
print "Maximum existing xref_id = $max_xref_id\n";
}
+
my $xref_id_offset = $max_xref_id + 1;
$self->xref_id_offset($xref_id_offset); #store
@@ -1885,7 +1886,7 @@ sub build_gene_display_xrefs {
my @transcripts = @{$genes_to_transcripts{$gene_id}};
- my $best_xref;
+ my $best_xref=undef;
my $best_xref_priority_idx = 99999;
my $best_transcript_length = -1;
foreach my $transcript_id (@transcripts) {
@@ -1917,7 +1918,7 @@ sub build_gene_display_xrefs {
}
}
- if ($best_xref) {
+ if (defined($best_xref)) {
# Write record
print GENE_DX "UPDATE gene g, analysis a SET g.display_xref_id=" . $best_xref . " WHERE g.gene_id=" . $gene_id . " AND g.analysis_id=a.analysis_id AND a.logic_name != \"ncRNA\";\n";
print GENE_DX_TXT $best_xref . "\t" . $gene_id ."\n";
@@ -2109,46 +2110,56 @@ sub do_upload {
my $core_db = $ensembl->dbc;
# xref.txt etc
- if(defined($self->delete_existing())){
-
- my $file = $ensembl->dir() . "/cleanup.sql";
- open(CLEAN,"<$file") || die "could not open $file for reading \n";
- while(<CLEAN>){
- chomp;
- my $sth = $core_db->prepare($_);
- $sth->execute() or die "Couldn't execute statement: " . $sth->errstr;
- }
- close CLEAN;
- #
- # used execute to make getting errors easier.
- # my $str = "mysql -u" .$core_db->username() ." -p" . $core_db->password() . " -h " . $core_db->host() ." -P " . $core_db->port() . " " .$core_db->dbname() . " < $file";
- # system $str;
-
-
-
- foreach my $table ("go_xref", "interpro") {
-
- my $sth = $core_db->prepare("DELETE FROM $table");
- print "Deleting existing data in $table\n";
- $sth->execute();
-
- }
- # gene & transcript display_xrefs
- my $sth = $core_db->prepare("UPDATE gene g, analysis a SET g.display_xref_id=NULL WHERE g.analysis_id=a.analysis_id AND a.logic_name != \"ncRNA\"");
- print "Setting all existing display_xref_id in gene to null\n";
+ my $file = $ensembl->dir() . "/cleanup.sql";
+ open(CLEAN,"<$file") || die "could not open $file for reading \n";
+ while(<CLEAN>){
+ chomp;
+ my $sth = $core_db->prepare($_);
+ $sth->execute() or die "Couldn't execute statement: " . $sth->errstr;
+ }
+ close CLEAN;
+
+
+ foreach my $table ("go_xref", "interpro") {
+
+ my $sth = $core_db->prepare("DELETE FROM $table");
+ print "Deleting existing data in $table\n";
$sth->execute();
+
+ }
+
+ # gene & transcript display_xrefs
+ my $sth = $core_db->prepare(<<GADES);
+ UPDATE gene g, analysis a
+ SET g.display_xref_id=NULL
+ WHERE g.analysis_id=a.analysis_id
+ AND a.logic_name != "ncRNA"
+GADES
+ print "Setting all existing display_xref_id in gene to null\n";
+ $sth->execute();
+
- my $sth = $core_db->prepare("UPDATE transcript t SET display_xref_id=NULL");
- print "Setting all existing display_xref_id in transcript to null\n";
- $sth->execute();
+ my $sth = $core_db->prepare(<<TRAN);
+ UPDATE transcript t, gene g, analysis a
+ SET t.display_xref_id=NULL
+ WHERE g.analysis_id = a.analysis_id
+ AND a.logic_name != "ncRNA"
+ AND g.gene_id =t.gene_id
+TRAN
+ print "Setting all existing display_xref_id in transcript to null\n";
+ $sth->execute();
- # gene descriptions
- my $sth = $core_db->prepare("UPDATE gene g, analysis a SET g.description=NULL WHERE g.analysis_id=a.analysis_id AND a.logic_name != \"ncRNA\"");
- print "Setting all existing descriptions in gene table to null\n";
- $sth->execute();
+ # gene descriptions
+ my $sth = $core_db->prepare(<<GENE);
+ UPDATE gene g, analysis a
+ SET g.description=NULL
+ WHERE g.analysis_id=a.analysis_id
+ AND a.logic_name != "ncRNA";
+GENE
+ print "Setting all existing descriptions in gene table to null\n";
+ $sth->execute();
- }
foreach my $table ("xref", "object_xref", "identity_xref", "external_synonym", "go_xref", "interpro") {
@@ -2170,13 +2181,6 @@ sub do_upload {
my $str = "mysql -u " .$core_db->username() ." -p" . $core_db->password() . " -h " . $core_db->host() ." -P " . $core_db->port() . " " .$core_db->dbname() . " < $file";
system $str;
- #$sth = $core_db->prepare("UPDATE $table SET display_xref_id=? WHERE ${table}_id=?");
- #open(DX_TXT, $file);
- #while (<DX_TXT>) {
- # my ($xref_id, $object_id) = split;
- # $sth->execute($xref_id, $object_id);
- #}
- #close(DX_TXT);
}
# gene descriptions
@@ -2197,19 +2201,6 @@ sub do_upload {
}
-# Delete (or set some fields to null) existing data
-
-sub delete_existing {
-
- my ($self, $arg) = @_;
-
- (defined $arg) &&
- ($self->{_delete_existing} = $arg );
- return $self->{_delete_existing};
-
-
-}
-
# Assign gene descriptions
# Algorithm:
# foreach gene
diff --git a/misc-scripts/xref_mapping/xref_mapper.pl b/misc-scripts/xref_mapping/xref_mapper.pl
index c1d033811a31ac23ddb5ccee22d2e056283cdd4c..4a26149efad617ea2f9cde5dfc41e3d89007a192 100644
--- a/misc-scripts/xref_mapping/xref_mapper.pl
+++ b/misc-scripts/xref_mapping/xref_mapper.pl
@@ -22,7 +22,6 @@ my $use_existing_mappings=undef;
my $maxdump=undef;
my $help;
my $upload = undef;
-my $deleteexisting;;
my $location;
GetOptions ('file=s' => \$file,
@@ -31,7 +30,6 @@ GetOptions ('file=s' => \$file,
'useexistingmappings' => \$use_existing_mappings,
'maxdump=n' => \$maxdump,
'upload' => \$upload,
- 'deleteexisting' => \$deleteexisting,
'location=s' => \$location,
'help' => sub { &show_help(); exit 1;} );
@@ -170,9 +168,6 @@ if(defined($species_hash{'species'})){
if(defined($maxdump)){
$mapper->maxdump($maxdump);
}
- if(defined($deleteexisting)){
- $mapper->delete_existing("yes");
- }
if(defined($use_existing_mappings)){
$mapper->use_existing_mappings("yes");
$mapper->dumpcheck("yes");