From 95fde0140ae51a5eb74875d3c4295f5d6469bec4 Mon Sep 17 00:00:00 2001
From: Ian Longden <ianl@sanger.ac.uk>
Date: Wed, 5 Nov 2008 15:44:37 +0000
Subject: [PATCH] new parsers
---
.../XrefParser/MGI_CCDS_Parser.pm | 134 ++++++++++
.../XrefParser/MGI_Desc_Parser.pm | 119 +++++++++
.../XrefParser/MGI_Vega_Parser.pm | 241 ++++++++++++++++++
.../MGI_curated_transcriptParser.pm | 181 +++++++++++++
4 files changed, 675 insertions(+)
create mode 100644 misc-scripts/xref_mapping/XrefParser/MGI_CCDS_Parser.pm
create mode 100644 misc-scripts/xref_mapping/XrefParser/MGI_Desc_Parser.pm
create mode 100644 misc-scripts/xref_mapping/XrefParser/MGI_Vega_Parser.pm
create mode 100644 misc-scripts/xref_mapping/XrefParser/MGI_curated_transcriptParser.pm
diff --git a/misc-scripts/xref_mapping/XrefParser/MGI_CCDS_Parser.pm b/misc-scripts/xref_mapping/XrefParser/MGI_CCDS_Parser.pm
new file mode 100644
index 0000000000..e829934ff4
--- /dev/null
+++ b/misc-scripts/xref_mapping/XrefParser/MGI_CCDS_Parser.pm
@@ -0,0 +1,134 @@
+package XrefParser::MGI_CCDS_Parser;
+
+use strict;
+
+use DBI;
+
+use base qw( XrefParser::BaseParser );
+
+# Parse file of HGNC records and assign direct xrefs
+# All assumed to be linked to genes
+
+
+if (!defined(caller())) {
+
+ if (scalar(@ARGV) != 1) {
+ print STDERR "\nUsage: MGI_CCDS_Parser.pm file <source_id> <species_id>\n\n";
+ exit(1);
+ }
+
+ run(@ARGV);
+}
+
+
+sub run_script {
+
+ my ($self, $file, $source_id, $species_id, $verbose) = @_;
+
+ my $wget = "";
+
+ if($file =~ /wget[=][>](\S+?)[,]/){
+ $wget = $1;
+ }
+
+
+ my %label;
+ my %version;
+ my %description;
+ my %accession;
+
+ my $dbi = $self->dbi();
+
+ my $sql = 'select source_id, priority_description from source where name like "MGI"';
+ my $sth = $dbi->prepare($sql);
+
+ $sth->execute();
+ my ($mgi_source_id, $desc);
+ $sth->bind_columns(\$mgi_source_id, \$desc);
+ my @arr;
+ while($sth->fetch()){
+ push @arr, $mgi_source_id;
+ }
+ $sth->finish;
+
+ $sql = "select accession, label, version, description from xref where source_id in (".join(", ",@arr).")";
+
+ $sth = $dbi->prepare($sql);
+ $sth->execute();
+ my ($acc, $lab, $ver, $desc);
+ $sth->bind_columns(\$acc, \$lab, \$ver, \$desc);
+ while (my @row = $sth->fetchrow_array()) {
+ if(defined($desc)){
+ $accession{$lab} = $acc;
+ $label{$acc} = $lab;
+ $version{$acc} = $ver;
+ $description{$acc} = $desc;
+ }
+ }
+ $sth->finish;
+
+
+
+ #
+ # Get master xref ids via the ccds label.
+ #
+
+ $sql = 'select x.label, x.xref_id from xref x, source s where x.source_id = s.source_id and s.name ="CCDS"';
+
+ my %ccds_label_to_xref_id;
+ $sth = $dbi->prepare($sql);
+ $sth->execute();
+ my ($xref_id);
+ $sth->bind_columns(\$lab, \$xref_id);
+ while (my @row = $sth->fetchrow_array()) {
+ $ccds_label_to_xref_id{$row[0]} = $row[1];
+ }
+ $sth->finish;
+
+
+
+ my $ua = LWP::UserAgent->new();
+ $ua->timeout(10);
+ $ua->env_proxy();
+
+
+ my $count = 0;
+ my $ccds_missing = 0;
+ my $entrezgene_missing = 0;
+
+ my $response = $ua->get($wget);
+
+ if ( !$response->is_success() ) {
+ die $response->status_line;
+ }
+ else{
+ #
+ #
+ ##chromosome g_accession gene gene_id ccds_id ccds_status cds_strand cds_from cds_to cds_locations match_type
+ #1 NC_000067.5 Xkr4 497097 CCDS14803.1 Public - 3206102 3661428 [3206102-3207048, 3411782-3411981, 3660632-3661428] Identical
+ #1 NC_000067.5 Rp1h 19888 CCDS14804.1 Public - 4334680 4342905 [4334680-4340171, 4341990-4342161, 4342282-4342905] Identical
+ my @lines = split(/\n/,$response->content);
+ foreach my $line (@lines){
+ my($chrom, $g_acc, $gene_name, $entrez_id, $ccds, @junk) = split(/\t/,$line);
+ if(defined($ccds_label_to_xref_id{$ccds})){
+ if(defined($accession{$gene_name}) and
+ defined($label{$accession{$gene_name}})){
+ my $acc = $accession{$gene_name};
+ $self->add_to_xrefs($ccds_label_to_xref_id{$ccds}, $acc, $version{$acc}, $label{$acc}, $description{$acc}, "", $source_id, $species_id);
+ $count++;
+ }
+ else{
+ $entrezgene_missing++;
+ }
+ }
+ else{
+ $ccds_missing++;
+ }
+ }
+ }
+ print "$ccds_missing ccds not resolved, $entrezgene_missing mgi not found. Added $count MGI xrefs via CCDS\n" if($verbose);
+
+}
+
+1;
+
diff --git a/misc-scripts/xref_mapping/XrefParser/MGI_Desc_Parser.pm b/misc-scripts/xref_mapping/XrefParser/MGI_Desc_Parser.pm
new file mode 100644
index 0000000000..5eeb670990
--- /dev/null
+++ b/misc-scripts/xref_mapping/XrefParser/MGI_Desc_Parser.pm
@@ -0,0 +1,119 @@
+package XrefParser::MGI_Desc_Parser;
+
+use strict;
+use File::Basename;
+
+use base qw( XrefParser::BaseParser );
+
+use strict;
+use Bio::EnsEMBL::DBSQL::DBAdaptor;
+
+
+#my $dbi2;
+
+if (!defined(caller())) {
+
+ if (scalar(@ARGV) != 1) {
+ print STDERR "\nUsage: MGI_Desc_Parser.pm file <source_id> <species_id>\n\n";
+ exit(1);
+ }
+
+ run(@ARGV);
+}
+
+sub run {
+
+ my $self = shift if (defined(caller(1)));
+
+ my $source_id = shift;
+ my $species_id = shift;
+ my $files = shift;
+ my $release_file = shift;
+ my $verbose = shift;
+
+ my $file = @{$files}[0];
+ my $syn_file = @{$files}[1];
+
+ if(!defined($source_id)){
+ $source_id = XrefParser::BaseParser->get_source_id_for_filename($file);
+ }
+ if(!defined($species_id)){
+ $species_id = XrefParser::BaseParser->get_species_id_for_filename($file);
+ }
+
+
+
+ my $mgi_io = $self->get_filehandle($file);
+
+ if ( !defined $mgi_io ) {
+ print STDERR "ERROR: Could not open $file\n";
+ return 1; # 1 is an error
+ }
+
+ my $xref_count =0;
+ my $syn_count =0;
+
+ my %acc_to_xref;
+#MGI Marker associations to Sequence (GenBank or RefSeq) information (tab-delimited)
+#MGI Marker Accession ID Marker Symbol Status Marker Type Marker Name cM Position Chromosome GenBank Accession IDs
+#(space-delimited) Unigene ID
+#(if any) RefSeq ID
+#(if any)
+ while ( $_ = $mgi_io->getline() ) {
+ chomp;
+ if($_ =~ /^ MGI:/){
+ my ($junk, $acc, $chr, $pos, $label, $status, @part_desc) = split(/\s+/,$_);
+
+ my $desc= join(" ",@part_desc);
+ $acc_to_xref{$acc} = $self->add_xref($acc,"",$label,$desc,$source_id,$species_id);
+ if($verbose and $desc eq ""){
+ print "$acc has no description\n";
+ }
+ $xref_count++;
+ }
+ }
+
+ $mgi_io->close();
+
+ print $xref_count." MGI Description Xrefs added\n" if($verbose);
+
+ #
+ # Now process the synonyms
+ #
+ my $mgi_io = $self->get_filehandle($syn_file);
+
+ if ( !defined $mgi_io ) {
+ print STDERR "ERROR: Could not open $file\n";
+ return 1; # 1 is an error
+ }
+
+
+ my $syn_count = 0;
+ while ( $_ = $mgi_io->getline() ) {
+ chomp;
+ if($_ =~ /^ MGI:/){
+
+ my ($junk, $acc, $chr, $pos, $symbol, @part_synonym) = split(/\s+/,$_);
+ my $syn = join(" ",@part_synonym);
+
+ if(defined($acc_to_xref{$acc})){
+ $self->add_synonym($acc_to_xref{$acc}, $syn);
+ $syn_count++;
+ }
+# Lots of withdrawn entrys.
+# else{
+# print "Could not find xref for $acc to add synonym $syn\n" if($verbose);
+# }
+ }
+ }
+ $mgi_io->close();
+ print $syn_count." synonyms added\n" if($verbose);
+
+ return 0; #successful
+}
+
+
+
+
+1;
+
diff --git a/misc-scripts/xref_mapping/XrefParser/MGI_Vega_Parser.pm b/misc-scripts/xref_mapping/XrefParser/MGI_Vega_Parser.pm
new file mode 100644
index 0000000000..a7fcf99b5d
--- /dev/null
+++ b/misc-scripts/xref_mapping/XrefParser/MGI_Vega_Parser.pm
@@ -0,0 +1,241 @@
+package XrefParser::MGI_Vega_Parser;
+
+use strict;
+use File::Basename;
+
+use base qw( XrefParser::BaseParser );
+
+use strict;
+use Bio::EnsEMBL::DBSQL::DBAdaptor;
+
+
+#my $dbi2;
+
+if (!defined(caller())) {
+
+ if (scalar(@ARGV) != 1) {
+ print STDERR "\nUsage: MGI_Vega_Parser.pm file <source_id> <species_id>\n\n";
+ exit(1);
+ }
+
+ run(@ARGV);
+}
+
+sub run_script {
+ my $self = shift if (defined(caller(1)));
+
+ my $file = shift;
+ my $source_id = shift;
+ my $species_id = shift;
+ my $verbose = shift;
+
+ my ($type, $my_args) = split(/:/,$file);
+
+ my $cuser = "ensro";
+ my $chost ="ens-staging";
+ my $cport = "3306";
+ my $cdbname = "";
+ my $cpass;
+
+ my $vuser = "ensro";
+ my $vhost ="ens-staging";
+ my $vport = "3306";
+ my $vdbname = "mus_musculus_vega_51_37d";
+ my $vpass;
+
+ if($my_args =~ /chost[=][>](\S+?)[,]/){
+ $chost = $1;
+ }
+ if($my_args =~ /cport[=][>](\S+?)[,]/){
+ $cport = $1;
+ }
+ if($my_args =~ /cdbname[=][>](\S+?)[,]/){
+ $cdbname = $1;
+ }
+ if($my_args =~ /cpass[=][>](\S+?)[,]/){
+ $cpass = $1;
+ }
+
+ if($my_args =~ /vhost[=][>](\S+?)[,]/){
+ $vhost = $1;
+ }
+ if($my_args =~ /vport[=][>](\S+?)[,]/){
+ $vport = $1;
+ }
+ if($my_args =~ /vdbname[=][>](\S+?)[,]/){
+ $vdbname = $1;
+ }
+ if($my_args =~ /vpass[=][>](\S+?)[,]/){
+ $vpass = $1;
+ }
+
+
+ my $xref_count = 0;
+
+
+ my $clone_source_id =
+ $self->get_source_id_for_source_name('Clone_based_vega_transcript');
+ my $curated_source_id =
+ $self->get_source_id_for_source_name('MGI_curated_transcript');
+
+
+ #
+ # need to get label and derscriptions fro primary acc.
+ #
+
+ my %mgi_to_label;
+ my %mgi_to_desc;
+ my %mgi_syn;
+
+ my $sth = $self->dbi()->prepare("SELECT x.accession, x.label, x.description from xref x, source s where x.source_id = s.source_id and s.name like 'MGI' and s.priority_description like 'descriptions'");
+
+ $sth->execute() or croak( $self->dbi()->errstr() );
+ while ( my @row = $sth->fetchrow_array() ) {
+ $mgi_to_label{$row[0]} = $row[1];
+ $mgi_to_desc{$row[0]} = $row[2];
+ }
+ $sth->finish;
+
+ #
+ # Also add synonyms
+ #
+
+ $sth = $self->dbi()->prepare("SELECT sy.synonym, x.accession from xref x, source s, synonym sy where sy.xref_id = x.xref_id and x.source_id = s.source_id and s.name like 'MGI' and s.priority_description like 'descriptions'");
+
+ $sth->execute() or croak( $self->dbi()->errstr() );
+ while ( my @row = $sth->fetchrow_array() ) {
+ $mgi_syn{$row[0]} = $row[1];
+ }
+ $sth->finish;
+
+
+
+
+ my $core_sql = 'select tsi.stable_id, x.dbprimary_acc from transcript_stable_id tsi, transcript t, object_xref ox, xref x, external_db e where tsi.transcript_id = t.transcript_id and ox.ensembl_id = t.transcript_id and ox.ensembl_object_type = "Transcript" and ox.xref_id = x.xref_id and x.external_db_id = e.external_db_id and e.db_name like "%OTTT"';
+
+
+ my %ott_to_enst;
+
+ my $dbi2 = $self->dbi2($chost, $cport, $cuser, $cdbname, $cpass);
+ if(!defined($dbi2)){
+ return 1;
+ }
+
+
+ $sth = $dbi2->prepare($core_sql);
+ $sth->execute() or croak( $dbi2->errstr() );
+ while ( my @row = $sth->fetchrow_array() ) {
+ $ott_to_enst{$row[1]} = $row[0];
+ }
+ $sth->finish;
+
+
+ #
+ # get the enst->ensg mappings.
+ #
+ my %enst_to_ensg;
+ $sth = $dbi2->prepare("select gsi.stable_id, tsi.stable_id from transcript t, gene_stable_id gsi, transcript_stable_id tsi where tsi.transcript_id = t.transcript_id and t.gene_id = gsi.gene_id");
+ $sth->execute() or croak( $dbi2->errstr() );
+ while ( my @row = $sth->fetchrow_array() ) {
+ $enst_to_ensg{$row[1]} = $row[0];
+ }
+ $sth->finish;
+
+
+ #
+ # Get the ott -> mgi mappings
+ #
+
+
+ my $vega_sql = (<<VSQL);
+ SELECT DISTINCT(tsi.stable_id) , x.dbprimary_acc, x.display_label
+ FROM transcript_stable_id tsi
+ INNER JOIN transcript t ON tsi.transcript_id = t.transcript_id
+ INNER JOIN gene g ON g.gene_id = t.gene_id
+ INNER JOIN object_xref ox ON ox.ensembl_id = g.gene_id
+ INNER JOIN xref x ON x.xref_id = ox.xref_id
+ INNER JOIN external_db e ON e.external_db_id = x.external_db_id
+ WHERE ox.ensembl_object_type = "Gene"
+ AND e.db_name like "MGI"
+VSQL
+
+ my $dbi3 = $self->dbi2($vhost, $vport, $vuser, $vdbname, $vpass);
+ if(!defined($dbi3)){
+ return 1;
+ }
+
+
+ my %seen;
+ $sth = $dbi3->prepare($vega_sql);
+ $sth->execute() or croak( $dbi3->errstr() );
+ while ( my @row = $sth->fetchrow_array() ) {
+ # [0] OTTMUST..., [1] MGI:123456 [2] Asx15 etc
+ my $desc= "";
+ my $prim_acc = $row[1];
+ if(defined($ott_to_enst{$row[0]})){
+ my $tran_stable_id = $ott_to_enst{$row[0]};
+ my $name = $prim_acc;
+ my $desc = "";
+ my $label = "";
+ if(defined($mgi_to_desc{$name})){
+ $desc = $mgi_to_desc{$name};
+ $label = $mgi_to_label{$name};
+ }
+ elsif( defined( $mgi_syn{$row[2]} ) and defined( $mgi_to_desc{$mgi_syn{$row[2]}})){ # synonym
+ $prim_acc = $mgi_syn{$row[2]};
+ $desc = $mgi_to_desc{$prim_acc};
+ $label = $mgi_to_label{$name};
+ }
+ else{
+ print "VEGA: $name [".$row[2]."} has no description\n" if($verbose);
+ }
+ my $xref_id = $self->add_xref($prim_acc, "" , $label , $desc, $source_id, $species_id);
+ my $ensg = $enst_to_ensg{$tran_stable_id};
+ if(!defined($seen{$xref_id.$ensg})){
+ $xref_count++;
+ $self->add_direct_xref($xref_id, $ensg , "Gene", "");
+ $seen{$xref_id.$ensg} = 1;
+ }
+ }
+ }
+
+ print "$xref_count direct xrefs succesfully parsed\n" if($verbose);
+
+
+# Done in the mapper
+# #
+# # Finally addd the synonyms
+# #
+
+# my $synonym_sql = (<<SYNO);
+#SELECT x2.xref_id, s.synonym
+# FROM synonym s
+# INNER JOIN xref x1 ON x1.xref_id = s.xref_id
+# INNER JOIN xref x2 ON x2.accession = x1.accession
+# INNER JOIN source s1 ON s1.source_id = x1.source_id
+# INNER JOIN source s2 ON s2.source_id = x2.source_id
+# WHERE x2.xref_id != x1.xref_id
+# AND s2.name = "MGI"
+# AND s2.priority_description = "vega"
+# AND s1.name = "MGI"
+# AND s1.priority_description = "descriptions"
+#SYNO
+
+# $sth = $self->dbi()->prepare($synonym_sql);
+
+# $sth->execute() or croak( $self->dbi()->errstr() );
+# while ( my @row = $sth->fetchrow_array() ) {
+# $self->add_synonym($row[0], $row[1]);
+# }
+# $sth->finish;
+
+
+return 0;
+}
+
+
+
+
+
+1;
+
diff --git a/misc-scripts/xref_mapping/XrefParser/MGI_curated_transcriptParser.pm b/misc-scripts/xref_mapping/XrefParser/MGI_curated_transcriptParser.pm
new file mode 100644
index 0000000000..d9f219c410
--- /dev/null
+++ b/misc-scripts/xref_mapping/XrefParser/MGI_curated_transcriptParser.pm
@@ -0,0 +1,181 @@
+package XrefParser::MGI_curated_transcriptParser;
+
+use strict;
+use File::Basename;
+
+use base qw( XrefParser::BaseParser );
+
+use strict;
+use Bio::EnsEMBL::DBSQL::DBAdaptor;
+
+
+#my $dbi2;
+
+if (!defined(caller())) {
+
+ if (scalar(@ARGV) != 1) {
+ print STDERR "\nUsage: MGI_curated_transcriptParser.pm file <source_id> <species_id>\n\n";
+ exit(1);
+ }
+
+ run(@ARGV);
+}
+
+sub run_script {
+ my $self = shift if (defined(caller(1)));
+
+ my $file = shift;
+ my $source_id = shift;
+ my $species_id = shift;
+ my $verbose = shift;
+
+ my ($type, $my_args) = split(/:/,$file);
+
+ my $cuser = "ensro";
+ my $chost ="ens-staging";
+ my $cport = "3306";
+ my $cdbname = "";
+ my $cpass;
+
+ my $vuser = "ensro";
+ my $vhost ="ens-staging";
+ my $vport = "3306";
+ my $vdbname = "mus_musculus_vega_51_37d";
+ my $vpass;
+
+ if($my_args =~ /chost[=][>](\S+?)[,]/){
+ $chost = $1;
+ }
+ if($my_args =~ /cport[=][>](\S+?)[,]/){
+ $cport = $1;
+ }
+ if($my_args =~ /cdbname[=][>](\S+?)[,]/){
+ $cdbname = $1;
+ }
+ if($my_args =~ /cpass[=][>](\S+?)[,]/){
+ $cpass = $1;
+ }
+
+ if($my_args =~ /vhost[=][>](\S+?)[,]/){
+ $vhost = $1;
+ }
+ if($my_args =~ /vport[=][>](\S+?)[,]/){
+ $vport = $1;
+ }
+ if($my_args =~ /vdbname[=][>](\S+?)[,]/){
+ $vdbname = $1;
+ }
+ if($my_args =~ /vpass[=][>](\S+?)[,]/){
+ $vpass = $1;
+ }
+
+
+ my $xref_count = 0;
+
+
+ my $clone_source_id =
+ $self->get_source_id_for_source_name('Clone_based_vega_transcript');
+ my $curated_source_id =
+ $self->get_source_id_for_source_name('MGI_curated_transcript');
+
+ my %name_to_mgi_number = %{ $self->get_label_to_acc( "MGI", $species_id ) };
+ my %name_to_mgi_desc = %{ $self->get_label_to_desc( "MGI", $species_id, "descriptions") };
+
+ my $core_sql = 'select tsi.stable_id, x.dbprimary_acc from transcript_stable_id tsi, transcript t, object_xref ox, xref x, external_db e where tsi.transcript_id = t.transcript_id and ox.ensembl_id = t.transcript_id and ox.ensembl_object_type = "Transcript" and ox.xref_id = x.xref_id and x.external_db_id = e.external_db_id and e.db_name like "%OTTT"';
+
+ my $vega_sql = 'select x.dbprimary_acc, x.display_label from xref x, external_db e where x.external_db_id = e.external_db_id and e.db_name like "Vega_transcript" and display_label not like "OTT%"';
+
+ my %ott_to_vega_name;
+ my %ott_to_enst;
+
+ my $dbi2 = $self->dbi2($chost, $cport, $cuser, $cdbname, $cpass);
+ if(!defined($dbi2)){
+ return 1;
+ }
+
+
+ my $sth = $dbi2->prepare($core_sql);
+ $sth->execute() or croak( $dbi2->errstr() );
+ while ( my @row = $sth->fetchrow_array() ) {
+ $ott_to_enst{$row[1]} = $row[0];
+ }
+ $sth->finish;
+
+ my $dbi3 = $self->dbi2($vhost, $vport, $vuser, $vdbname, $vpass);
+ if(!defined($dbi3)){
+ return 1;
+ }
+
+
+ $sth = $dbi3->prepare($vega_sql);
+ $sth->execute() or croak( $dbi3->errstr() );
+ while ( my @row = $sth->fetchrow_array() ) {
+ # [0] OTTMUST..., [1] Mrpl15-001 etc
+ my $desc= "";
+ if(defined($ott_to_enst{$row[0]})){
+ my $id = $curated_source_id;
+ my $name = $row[1];
+ $name =~ s/^WU://;
+ my $prim_acc = $name;
+ my $stable_id = $ott_to_enst{$row[0]};
+ if($name =~ /[.]/){
+ $id = $clone_source_id;
+ }
+ else{
+ my $mgi_name = $name;
+ # find MGI name
+ my($mgi_bit, $num) = split(/-\d\d\d/,$name);
+ if(defined($name_to_mgi_number{$mgi_bit})){
+ $prim_acc = $name_to_mgi_number{$mgi_bit};
+ }
+ if(defined($name_to_mgi_desc{$mgi_bit})){
+ $desc = $name_to_mgi_desc{$mgi_bit};
+ }
+ else{
+ print "$mgi_bit has no description\n" if($verbose);
+ }
+ }
+ my $xref_id = $self->add_xref($prim_acc, "" , $name , $desc, $id, $species_id);
+ $xref_count++;
+
+ $self->add_direct_xref($xref_id, $ott_to_enst{$row[0]}, "Transcript", "");
+
+
+ }
+ }
+
+ print "$xref_count direct xrefs succesfully parsed\n" if($verbose);
+
+ #Finally add the synonyms:-
+ my $synonym_sql = (<<SYNO);
+SELECT x2.xref_id, s.synonym
+ FROM synonym s
+ INNER JOIN xref x1 ON x1.xref_id = s.xref_id
+ INNER JOIN xref x2 ON x2.accession = x1.accession
+ INNER JOIN source s1 ON s1.source_id = x1.source_id
+ INNER JOIN source s2 ON s2.source_id = x2.source_id
+ WHERE x2.xref_id != x1.xref_id
+ AND s2.name = "MGI_curated_transcript"
+ AND s1.name = "MGI"
+ AND s1.priority_description = "descriptions"
+SYNO
+
+
+ $sth = $self->dbi()->prepare($synonym_sql);
+
+ $sth->execute() or croak( $self->dbi()->errstr() );
+ while ( my @row = $sth->fetchrow_array() ) {
+ $self->add_synonym($row[0], $row[1]);
+ }
+ $sth->finish;
+
+
+ return 0;
+}
+
+
+
+
+
+1;
+
--
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