From 148b371072f2676846ee8f1e3f4c6aa72fa63f91 Mon Sep 17 00:00:00 2001
From: Ian Longden <ianl@sanger.ac.uk>
Date: Mon, 5 Sep 2011 15:36:56 +0000
Subject: [PATCH] general tidy
---
.../xref_mapping/XrefMapper/Interpro.pm | 110 ++++++++++++------
1 file changed, 76 insertions(+), 34 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefMapper/Interpro.pm b/misc-scripts/xref_mapping/XrefMapper/Interpro.pm
index 0cb4fd6d86..81dee341bd 100644
--- a/misc-scripts/xref_mapping/XrefMapper/Interpro.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/Interpro.pm
@@ -1,10 +1,11 @@
package XrefMapper::Interpro;
+use strict;
+use warnings;
use vars '@ISA';
@ISA = qw{ XrefMapper::BasicMapper };
-use strict;
-use warnings;
+
use XrefMapper::BasicMapper;
sub new {
@@ -34,18 +35,47 @@ sub process{
$object_xref_id++;
- my $add_object_xref_sth = $self->xref->dbc->prepare('insert into object_xref (object_xref_id, ensembl_id,ensembl_object_type, xref_id, linkage_type, ox_status, master_xref_id ) values (?, ?, ?, ?, ?, "DUMP_OUT", ?)');
+
+#
+# Get the sql and sths required.
+#
+
+ my $add_ox_sql = (<<"AOX");
+INSERT INTO object_xref
+ (object_xref_id, ensembl_id,ensembl_object_type, xref_id,
+ linkage_type, ox_status, master_xref_id )
+ VALUES (?, ?, ?, ?, ?, "DUMP_OUT", ?)
+AOX
+ my $add_object_xref_sth = $self->xref->dbc->prepare($add_ox_sql);
+
+
+ my $add_go_xref_sql = (<<"AGX");
+INSERT INTO go_xref (object_xref_id, linkage_type)
+ VALUES (?, ?)
+AGX
+ my $add_go_xref_sth = $self->xref->dbc->prepare($add_go_xref_sql);
+
+ my $ins_ix_sql = (<<"IXS");
+INSERT INTO identity_xref (object_xref_id, query_identity, target_identity)
+ VALUES (?, 100, 100)
+IXS
+ my $ins_ix_sth = $self->xref->dbc->prepare($ins_ix_sql);
+
+ my $dep_sql = (<<"DLS");
+SELECT dependent_xref_id, linkage_annotation
+ FROM dependent_xref
+ WHERE master_xref_id = ?
+DLS
+ my $dep_sth = $self->xref->dbc->prepare($dep_sql);
+
local $add_object_xref_sth->{RaiseError}; #catch duplicates
local $add_object_xref_sth->{PrintError}; # cut down on error messages
-
- my $add_go_xref_sth = $self->xref->dbc->prepare('insert into go_xref (object_xref_id, linkage_type) values (?, ?)');
- my $ins_ix_sth = $self->xref->dbc->prepare("insert into identity_xref (object_xref_id, query_identity, target_identity) values(?, 100, 100)");
# Get a mapping of protein domains to ensembl translations for
# interpro dependent xrefs
- my $core_sql = "SELECT hit_name, translation_id FROM protein_feature" ;
+ my $core_sql = 'SELECT hit_name, translation_id FROM protein_feature' ;
my $core_sth = $self->core->dbc->prepare($core_sql);
$core_sth->execute();
my %domain_to_translation = ();
@@ -56,26 +86,35 @@ sub process{
push @{$domain_to_translation{$domain}}, $translation;
}
- my $dep_sth = $self->xref->dbc->prepare("select dependent_xref_id, linkage_annotation from dependent_xref where master_xref_id = ?");
-
- # Get a list of interpro data, including dependent xrefs if avail
- $sth = $self->xref->dbc->prepare("
- SELECT ip.interpro, ip.pfam, x2.xref_id, x2.source_id,
- dx.linkage_annotation, dx.master_xref_id
- FROM interpro ip, xref x
- LEFT JOIN dependent_xref dx ON x.xref_id=dx.master_xref_id
- LEFT JOIN xref x2 ON dx.dependent_xref_id=x2.xref_id
- WHERE ip.interpro = x.accession and ip.dbtype != 'PRINTS'");
+
+ my $int_sql = (<<"ISQ");
+SELECT ip.interpro, ip.pfam, x2.xref_id, x2.source_id,
+ dx.linkage_annotation, dx.master_xref_id
+ FROM interpro ip, xref x
+ LEFT JOIN dependent_xref dx
+ ON x.xref_id=dx.master_xref_id
+ LEFT JOIN xref x2
+ ON dx.dependent_xref_id=x2.xref_id
+ WHERE ip.interpro = x.accession and ip.dbtype != 'PRINTS'
+ISQ
+ $sth = $self->xref->dbc->prepare($int_sql);
+
+
my $rv = $sth->execute();
-# my %interpro_cache;
- my %added;
+
+# my %added;
my $dup=0;
while( my $row = $sth->fetchrow_arrayref() ){
my ( $interpro, $pfam, $dx_xref_id, $dx_source_id, $go_linkage, $master_id ) = @$row;
if( $dx_xref_id ){
foreach my $ensembl_id( @{$domain_to_translation{$pfam}||[]} ){
#...And the interpro domain maps to a translation
- $add_object_xref_sth->execute($object_xref_id, $ensembl_id, 'Translation', $dx_xref_id, 'DEPENDENT', $master_id);
+ $add_object_xref_sth->execute($object_xref_id,
+ $ensembl_id,
+ 'Translation',
+ $dx_xref_id,
+ 'DEPENDENT',
+ $master_id);
if($add_object_xref_sth->err){
my $err = $add_object_xref_sth->errstr;
if($err =~ /Duplicate/){
@@ -87,7 +126,6 @@ sub process{
}
}
$ins_ix_sth->execute($object_xref_id);
- $added{$dx_source_id}++;
$oxref_count++;
if($go_linkage){
$add_go_xref_sth->execute($object_xref_id, $go_linkage );
@@ -107,15 +145,20 @@ sub process{
my $dep_xref_id;
my $link;
$dep_sth->bind_columns(\$dep_xref_id, \$link);
- while($dep_sth->fetch()){
- $add_object_xref_sth->execute($object_xref_id, $ensembl_id, 'Translation', $dep_xref_id, 'DEPENDENT', $new_master_id);
+ while($dep_sth->fetch()){
+ $add_object_xref_sth->execute($object_xref_id,
+ $ensembl_id,
+ 'Translation',
+ $dep_xref_id,
+ 'DEPENDENT',
+ $new_master_id);
if(!$add_object_xref_sth->err){
push @master_xref_ids, $dep_xref_id;
if($link){
$add_go_xref_sth->execute($object_xref_id, $link );
}
$ins_ix_sth->execute($object_xref_id);
- }
+ }
$object_xref_id++;
}
}
@@ -127,16 +170,15 @@ sub process{
}
}
$sth->finish();
-
-
- print "\n".$dup." already existed\n\n" if($self->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{$key}. " object xrefs added\n";
-# }
+
+
+ if($self->verbose){
+ print "\n".$dup." already existed\n\n";
+ print " Wrote $ipro_count interpro table entries\n";
+ print " including $oxref_count object xrefs, \n";
+ print " and $goxref_count go xrefs\n";
+ }
+ return;
}
1;
--
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