From 454cac5d3a91ea6546dd9ffcc8872ddf9a0e238f Mon Sep 17 00:00:00 2001
From: Ian Longden <ianl@sanger.ac.uk>
Date: Tue, 24 May 2011 14:30:13 +0000
Subject: [PATCH] add the synonyms
---
.../xref_mapping/XrefParser/RGDParser.pm | 18 ++++++++++++++++--
1 file changed, 16 insertions(+), 2 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefParser/RGDParser.pm b/misc-scripts/xref_mapping/XrefParser/RGDParser.pm
index 03d8db730d..a35e5deef5 100644
--- a/misc-scripts/xref_mapping/XrefParser/RGDParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/RGDParser.pm
@@ -43,6 +43,7 @@ sub run {
$species_id = XrefParser::BaseParser->get_species_id_for_filename($file);
}
+ my $dbi = $self->dbi();
my (%refseq) = %{XrefParser::BaseParser->get_valid_codes("refseq",$species_id)};
@@ -79,12 +80,19 @@ sub run {
if($linearr[23] ne "GENBANK_NUCLEOTIDE"){
die ("GENBANK_NUCLEOTIDE is not the twentysixth element in the header but ".$linearr[23]." is.\\n");
}
+ if($linearr[29] ne "OLD_SYMBOL"){
+ die ("NAME is not the third element in the header\n$line\n");
+ }
+
+ my $sql = "insert into synonym (xref_id, synonym) values (?, ?)";
+ my $add_syn_sth = $dbi->prepare($sql);
my $count= 0;
my $mismatch = 0;
+ my $syn_count = 0;
while ( $line = $rgd_io->getline() ) {
chomp $line;
- my ($rgd, $symbol, $name, $refseq) = (split (/\t/,$line))[0,1,2,23];
+ my ($rgd, $symbol, $name, $refseq,$old_name) = (split (/\t/,$line))[0,1,2,23,29];
my @nucs = split(/\;/,$refseq);
my $done = 0;
my $failed_list ="";
@@ -94,8 +102,13 @@ sub run {
$xref=$refseq{$nuc} if defined($refseq{$nuc});
if(defined($xref)){
$done = 1;
- XrefParser::BaseParser->add_to_xrefs($xref,$rgd,"",$symbol,$name,"",$source_id,$species_id);
+ my $xref_id = XrefParser::BaseParser->add_to_xrefs($xref,$rgd,"",$symbol,$name,"",$source_id,$species_id);
$count++;
+ my @syns = split(/\;/,$old_name);
+ foreach my $syn(@syns){
+ $add_syn_sth->execute($xref_id, $syn);
+ $syn_count++;
+ }
}
else{
$failed_list .= " $nuc";
@@ -115,6 +128,7 @@ sub run {
print "\t$count xrefs succesfully loaded and dependent on refseq\n" if($verbose);
print "\t$mismatch xrefs added but with NO dependencies\n" if($verbose);
+ print "added $syn_count synonyms\n" if($verbose);
return 0;
}
--
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