From 47e090560749376ac370f8bb3a711592634edfbb Mon Sep 17 00:00:00 2001
From: Ian Sealy <is1@sanger.ac.uk>
Date: Thu, 16 Jun 2005 13:25:30 +0000
Subject: [PATCH] ZFINParser.pm now actually stores Xrefs. Modified GOParser.pm
to handle ZFIN.
---
.../xref_mapping/XrefParser/GOParser.pm | 63 ++++++++++++-------
.../xref_mapping/XrefParser/ZFINParser.pm | 3 +-
2 files changed, 41 insertions(+), 25 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefParser/GOParser.pm b/misc-scripts/xref_mapping/XrefParser/GOParser.pm
index ec63672562..e54bea84e3 100644
--- a/misc-scripts/xref_mapping/XrefParser/GOParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/GOParser.pm
@@ -45,6 +45,8 @@ sub run {
my (%refseq) = %{XrefParser::BaseParser->get_valid_codes("refseq",$species_id)};
my %worm;
my $wormset;
+ my %fish;
+ my $fishset;
my $count = 0;
@@ -59,39 +61,52 @@ sub run {
$array[9] =~ s/\'/\\\'/g;
my $master=0;
if($array[0] =~ /ENSEMBL/){
- #these might be good for a check
- # match GO to Uniprot
- # match Uniprot to ENSEMBL
- # check ENSEMBL's are the same.
+ #these might be good for a check
+ # match GO to Uniprot
+ # match Uniprot to ENSEMBL
+ # check ENSEMBL's are the same.
}
elsif($array[0] =~ /RefSeq/){
- if($refseq{$array[1]}){
- XrefParser::BaseParser->add_to_xrefs($refseq{$array[1]},$array[4],'',$array[4],'',$array[6],$source_id,$species_id);
- $count++;
- }
+ if($refseq{$array[1]}){
+ XrefParser::BaseParser->add_to_xrefs($refseq{$array[1]},$array[4],'',$array[4],'',$array[6],$source_id,$species_id);
+ $count++;
+ }
}
elsif($array[0] =~ /UniProt/){
- if($swiss{$array[1]}){
- XrefParser::BaseParser->add_to_xrefs($swiss{$array[1]},$array[4],'',$array[4],'',$array[6],$source_id,$species_id);
- $count++;
- }
+ if($swiss{$array[1]}){
+ XrefParser::BaseParser->add_to_xrefs($swiss{$array[1]},$array[4],'',$array[4],'',$array[6],$source_id,$species_id);
+ $count++;
+ }
}
elsif($array[0] =~ /^WB$/){
#WB CE20707 ZYG-9 GO:0008017 WB:WBPaper00003099|PMID:9606208 ISS F protein taxon:6239 20030829 WB
- if(!defined($wormset)){
- $wormset = 1;
- %worm = %{XrefParser::BaseParser->get_valid_xrefs_for_dependencies
- ('wormbase_transcript','Uniprot/SPTREMBL','RefSeq_peptide',
- 'Uniprot/SWISSPROT')};
- }
- if(defined($worm{$array[2]})){
- XrefParser::BaseParser->add_to_xrefs($worm{$array[2]},$array[4],'',$array[4],'',$array[6],$source_id,$species_id);
- $count++;
- }
+ if(!defined($wormset)){
+ $wormset = 1;
+ %worm = %{XrefParser::BaseParser->get_valid_xrefs_for_dependencies
+ ('wormbase_transcript','Uniprot/SPTREMBL','RefSeq_peptide',
+ 'Uniprot/SWISSPROT')};
+ }
+ if(defined($worm{$array[2]})){
+ XrefParser::BaseParser->add_to_xrefs($worm{$array[2]},$array[4],'',$array[4],'',$array[6],$source_id,$species_id);
+ $count++;
+ }
+ }
+ elsif($array[0] =~ /^ZFIN$/){
+#ZFIN ZDB-GENE-030131-5418 rfng GO:0030902 ZFIN:ZDB-PUB-050125-4|PMID:15659486 IMP ZFIN:ZDB-MRPHLNO-050308-5 radical fringe homolog (Drosophila) gene taxon:7955 20050310 ZFIN
+ if(!defined($fishset)){
+ $fishset = 1;
+ %fish = %{XrefParser::BaseParser->get_valid_xrefs_for_dependencies
+ ('ZFIN_ID','Uniprot/SPTREMBL','RefSeq_peptide',
+ 'Uniprot/SWISSPROT')};
+ }
+ if(defined($fish{$array[1]})){
+ XrefParser::BaseParser->add_to_xrefs($fish{$array[1]},$array[4],'',$array[4],'',$array[6],$source_id,$species_id);
+ $count++;
+ }
}
elsif(!defined($wrongtype{$array[0]})){
- print STDERR "WARNING: unknown type ".$array[0]."\n";
- $wrongtype{$array[0]} = 1;
+ print STDERR "WARNING: unknown type ".$array[0]."\n";
+ $wrongtype{$array[0]} = 1;
}
}
}
diff --git a/misc-scripts/xref_mapping/XrefParser/ZFINParser.pm b/misc-scripts/xref_mapping/XrefParser/ZFINParser.pm
index 156b58b4ea..2addd3d1cd 100644
--- a/misc-scripts/xref_mapping/XrefParser/ZFINParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/ZFINParser.pm
@@ -58,6 +58,7 @@ sub run {
chomp;
my ($zfin, $label, $acc) = split (/\s+/,$_);
if(defined($swiss{$acc})){
+ XrefParser::BaseParser->add_to_xrefs($swiss{$acc},$zfin,'',$label,'','',$source_id,$species_id);
$count++;
}
else{
@@ -74,6 +75,7 @@ sub run {
chomp;
my ($zfin, $label, $acc) = split (/\s+/,$_);
if(defined($refseq{$acc})){
+ XrefParser::BaseParser->add_to_xrefs($refseq{$acc},$zfin,'',$label,'','',$source_id,$species_id);
$count++;
}
else{
@@ -83,7 +85,6 @@ sub run {
close REFSEQ;
print "\t$count xrefs succesfully loaded\n";
print "\t$mismatch xrefs ignored\n";
- die "Do not store loaded bit (NOT tested yet)\n";
}
sub new {
--
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