From 6c49467bfce89c84f9a2b770b3919bded75902a4 Mon Sep 17 00:00:00 2001
From: Ian Longden <ianl@sanger.ac.uk>
Date: Tue, 29 Mar 2005 10:51:28 +0000
Subject: [PATCH] add dependent xref if worm transcript not found and swissprot
is given
---
.../xref_mapping/XrefParser/WormPepParser.pm | 39 ++++++++++---------
1 file changed, 20 insertions(+), 19 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefParser/WormPepParser.pm b/misc-scripts/xref_mapping/XrefParser/WormPepParser.pm
index 94db886a16..446f722dae 100644
--- a/misc-scripts/xref_mapping/XrefParser/WormPepParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/WormPepParser.pm
@@ -38,27 +38,27 @@ sub run {
if(!defined($species_id)){
$species_id = XrefParser::BaseParser->get_species_id_for_filename($file);
}
- my %worm = %{XrefParser::BaseParser->get_valid_xrefs_for_dependencies
- ('wormbase_transcript','Uniprot/SPTREMBL','RefSeq_peptide',
- 'Uniprot/SWISSPROT')};
- my $sql = "update xref set accession =\'?\' where xref_id=?";
+
+ my (%worm) = %{XrefParser::BaseParser->get_valid_codes("wormbase_transcript",$species_id)};
+
+ my (%swiss) = %{XrefParser::BaseParser->get_valid_codes("Uniprot",$species_id)};
+
+ my $sql = "update xref set accession =? where xref_id=?";
my $dbi = XrefParser::BaseParser->dbi();
my $sth = $dbi->prepare($sql);
- my $count = 0;
-
open(PEP,"<".$file) || die "Could not open $file\n";
while (<PEP>) {
- my ($transcript, $wb, $swiss) = (split(/\t/,substr($_,1)))[0,1,5];
+ my ($transcript, $wb, $swiss_ref) = (split(/\t/,substr($_,1)))[0,1,5];
- if($swiss =~ /SW:(.*)/){
- $swiss = $1;
+ if($swiss_ref =~ /SW:(.*)/){
+ $swiss_ref = $1;
+ }
+ else{
+ $swiss_ref = 0 ;
}
-# else{
-# print "ERR:".$_;
-# }
if(length($wb) < 3){
print "ERRR:".$_;
}
@@ -81,21 +81,22 @@ sub run {
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 $gene (".$worm{$gene}.") to $transcript\n";
+ print "changing $gene to $transcript\n";
}
# if no record exists for this
elsif(!defined($worm{$gene}) and !defined($worm{$transcript})){
- print "Could not find: $transcript ????";
- if($swiss){
- print " on sw: $swiss";
+ if($swiss_ref){
+ if(defined($swiss{$swiss_ref})){
+ XrefParser::BaseParser->add_to_xrefs($swiss{$swiss_ref},$transcript,'',$transcript,"","",$source_id,$species_id);
+ }
+ else{
+ print $swiss_ref." not found\n";
+ }
}
- print "\n";
}
-# print $gene,"\t",$swiss,"\t",$wb,"\n";
}
-# die "Just testing at the moment\n";
}
--
GitLab