From ce5aa54a1cd0141d0db919ae52d378eaa2d00112 Mon Sep 17 00:00:00 2001
From: Ian Longden <ianl@sanger.ac.uk>
Date: Thu, 31 Mar 2005 13:53:26 +0000
Subject: [PATCH] Removed wormbase info as this will now be obtained only from
the wormbase file
---
.../XrefParser/RefSeqGPFFParser.pm | 18 ----------
.../xref_mapping/XrefParser/UniProtParser.pm | 36 -------------------
2 files changed, 54 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefParser/RefSeqGPFFParser.pm b/misc-scripts/xref_mapping/XrefParser/RefSeqGPFFParser.pm
index 1aa5722b65..6683dbffaf 100644
--- a/misc-scripts/xref_mapping/XrefParser/RefSeqGPFFParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/RefSeqGPFFParser.pm
@@ -155,7 +155,6 @@ sub create_xrefs {
my @LocusIDline = $entry =~ /db_xref=.LocusID:(\d+)/g;
my @EntrezGeneIDline = $entry =~ /db_xref=.GeneID:(\d+)/g;
my @mimline = $entry =~ /db_xref=.MIM:(\d+)/g;
- my @wormline = $entry =~ /db_xref=\"WormBase:(\S+)\"/g;
foreach my $ll (@LocusIDline) {
my %dep;
@@ -164,23 +163,6 @@ sub create_xrefs {
$dep{ACCESSION} = $ll;
push @{$xref->{DEPENDENT_XREFS}}, \%dep;
}
- foreach my $ll (@wormline) {
- my %dep;
- $dep{SOURCE_ID} = $dependent_sources{'wormbase_transcript'};
- $dep{LINKAGE_SOURCE_ID} = $source_id;
- $dep{ACCESSION} = $ll;
- $dep{LABEL} = $ll;
- push @{$xref->{DEPENDENT_XREFS}}, \%dep;
- if($ll =~ /(\S+\.\d+)/){
- my $temp = $1;
- my %dep2;
- $dep2{SOURCE_ID} = $dependent_sources{'wormbase_gene'};
- $dep2{LINKAGE_SOURCE_ID} = $source_id;
- $dep2{ACCESSION} = $temp;
- $dep2{LABEL} = $temp;
- push @{$xref->{DEPENDENT_XREFS}}, \%dep2;
- }
- }
foreach my $ll (@EntrezGeneIDline) {
my %dep;
$dep{SOURCE_ID} = $dependent_sources{EntrezGene};
diff --git a/misc-scripts/xref_mapping/XrefParser/UniProtParser.pm b/misc-scripts/xref_mapping/XrefParser/UniProtParser.pm
index e296e33b5a..4019a8d5b8 100644
--- a/misc-scripts/xref_mapping/XrefParser/UniProtParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/UniProtParser.pm
@@ -245,42 +245,6 @@ sub create_xrefs {
}
}
}
- elsif($source =~ /WormPep/){
- #DR WormPep; F35D6.1b; CE28299.
- my %dep;
- $dep{SOURCE_NAME} = 'wormbase_transcript';
- $dep{LINKAGE_SOURCE_ID} = $xref->{SOURCE_ID};
- $dep{SOURCE_ID} = $dependent_sources{'wormbase_transcript'};
- $dep{ACCESSION} = $acc;
- $dep{LABEL} = $acc;
- push @{$xref->{DEPENDENT_XREFS}}, \%dep; # array of hashrefs
-
- my $gene;
- if($acc =~ /(\S+\.\d+)/){
- $gene = $1;
- my %dep2;
- $dep2{SOURCE_NAME} = 'wormbase_gene';
- $dep2{LINKAGE_SOURCE_ID} = $xref->{SOURCE_ID};
- $dep2{SOURCE_ID} = $dependent_sources{'wormbase_gene'};
- $dep2{ACCESSION} = $gene;
- $dep2{LABEL} = $gene;
- push @{$xref->{DEPENDENT_XREFS}}, \%dep2; # array of hashrefs
- }
-
- my %dep3;
- my $worm_id ;
- if($extra[0] =~ /([^.]+)/){
- $worm_id = $1;
- }
- $dep3{SOURCE_NAME} = 'wormpep_id';
- $dep3{LINKAGE_SOURCE_ID} = $xref->{SOURCE_ID};
- $dep3{SOURCE_ID} = $dependent_sources{'wormpep_id'};
- $dep3{ACCESSION} = $worm_id;
- $dep3{LABEL} = $worm_id;
- push @{$xref->{DEPENDENT_XREFS}}, \%dep3; # array of hashrefs
-
-# print $worm_id."\t".$gene."\t".$acc."\n";
- }
}
}
--
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