From d5b9c8455a3b2dbe31b36f4a1280f5efe0843c20 Mon Sep 17 00:00:00 2001
From: Ian Longden <ianl@sanger.ac.uk>
Date: Tue, 29 Mar 2005 14:27:44 +0000
Subject: [PATCH] reworked to work correctly
---
.../xref_mapping/XrefParser/WormPepParser.pm | 90 +++++++++++--------
1 file changed, 51 insertions(+), 39 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefParser/WormPepParser.pm b/misc-scripts/xref_mapping/XrefParser/WormPepParser.pm
index 446f722dae..62596a5694 100644
--- a/misc-scripts/xref_mapping/XrefParser/WormPepParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/WormPepParser.pm
@@ -39,6 +39,8 @@ sub run {
$species_id = XrefParser::BaseParser->get_species_id_for_filename($file);
}
+ my $worm_source_id = XrefParser::BaseParser->get_source_id_for_source_name('wormbase_transcript');
+
my (%worm) = %{XrefParser::BaseParser->get_valid_codes("wormbase_transcript",$species_id)};
my (%swiss) = %{XrefParser::BaseParser->get_valid_codes("Uniprot",$species_id)};
@@ -48,56 +50,66 @@ sub run {
my $sth = $dbi->prepare($sql);
+ my $sql2 = "select x2.accession, x2.xref_id ";
+ $sql2 .= "from dependent_xref d, xref x1, xref x2 ";
+ $sql2 .= "where d.master_xref_id = x1.xref_id and ";
+ $sql2 .= " d.dependent_xref_id = x2.xref_id and ";
+ $sql2 .= " x2.source_id = $worm_source_id and ";
+ $sql2 .= " x1.xref_id = ? and ";
+ $sql2 .= " x2.accession = ?";
+ my $sth2 = $dbi->prepare($sql2);
+
+
+ my $sql3 = 'delete from dependent_xref where dependent_xref.master_xref_id=? and dependent_xref.dependent_xref_id=?';
+ my $sth3 = $dbi->prepare($sql3);
+
open(PEP,"<".$file) || die "Could not open $file\n";
while (<PEP>) {
my ($transcript, $wb, $swiss_ref) = (split(/\t/,substr($_,1)))[0,1,5];
-
+ my $swiss_xref;
if($swiss_ref =~ /SW:(.*)/){
$swiss_ref = $1;
- }
- else{
- $swiss_ref = 0 ;
- }
- if(length($wb) < 3){
- print "ERRR:".$_;
- }
-
- #Is the transcript different from the gene
- my $diff =0;
- my $gene;
- if($transcript =~ /(\S+\.\d+)/){
- $gene = $1;
- if($gene ne $transcript){
- $diff=1;
- }
- }
- else{
- die "Gene format not recognised $transcript\n";
- }
-
- my $exists =0;
- # if gene stored as transcript so change this
- if(defined($worm{$gene}) and !defined($worm{$transcript})){
- # change accesion to transcript name instead of gene
- $sth->execute($transcript, $worm{$gene}) || die $dbi->errstr;
- print "changing $gene to $transcript\n";
- }
- # if no record exists for this
- elsif(!defined($worm{$gene}) and !defined($worm{$transcript})){
- if($swiss_ref){
- if(defined($swiss{$swiss_ref})){
- XrefParser::BaseParser->add_to_xrefs($swiss{$swiss_ref},$transcript,'',$transcript,"","",$source_id,$species_id);
+ if(defined($swiss{$swiss_ref})){
+ $swiss_xref = $swiss{$swiss_ref};
+ my $diff =0;
+ my $gene;
+ if($transcript =~ /(\S+\.\d+)/){
+ $gene = $1;
+ if($gene ne $transcript){
+ $diff=1;
+ }
}
else{
- print $swiss_ref." not found\n";
- }
+ die "Gene format not recognised $transcript\n";
+ }
+
+ $sth2->execute($swiss_xref, $gene) || die $dbi->errstr;
+ (my $gene_acc, my $gene_xref) = $sth2->fetchrow_array();
+
+ $sth2->execute($swiss_xref, $transcript) || die $dbi->errstr;
+ (my $tran_acc, my $tran_xref) = $sth2->fetchrow_array();
+
+ my $create = 1;
+ if(defined($tran_xref)){ #okay
+ $create = 0;
+ }
+ elsif(defined($gene_xref)){
+ #need to delete dependency
+ #then add new one with correct name
+ $sth3->execute($swiss_xref, $gene_xref) || die $dbi->errstr;
+ print "removing $swiss_ref -> $gene : ";
+ }
+ if($create){
+ XrefParser::BaseParser->add_to_xrefs($swiss_xref,$transcript,'',$transcript,"","",$source_id,$species_id);
+ print "adding $swiss_ref -> $transcript\n";
+ }
+
}
- }
-
+ }
}
-
+
}
--
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