From e259222a322a86fcbfd1190700ee73499857b887 Mon Sep 17 00:00:00 2001
From: Emmanuel Mongin <mongin@sanger.ac.uk>
Date: Fri, 13 Jun 2003 13:46:22 +0000
Subject: [PATCH] added GKB mapping
---
misc-scripts/protein_match/get_Xmapping.pl | 17 ++++++++++++++++-
misc-scripts/protein_match/mapping_conf.pl | 5 +++++
misc-scripts/protein_match/maps2db.pl | 6 ------
3 files changed, 21 insertions(+), 7 deletions(-)
diff --git a/misc-scripts/protein_match/get_Xmapping.pl b/misc-scripts/protein_match/get_Xmapping.pl
index 09b29f67a3..8254dbd407 100644
--- a/misc-scripts/protein_match/get_Xmapping.pl
+++ b/misc-scripts/protein_match/get_Xmapping.pl
@@ -26,7 +26,8 @@ my $refseq_gnp = $conf{'refseq_gnp'};
my $ens1 = $conf{'ens1'};
my $ens4 = $conf{'ens4'};
my $refseq_pred = $conf{'refseq_pred_gnp'};
-my $go = $conf{'go'};
+my $go = $conf{'go'};
+my $gkb = $conf{'gkb'};
#Get specific options for the mouse
my $mgi_sp = $conf{'mgi_sp'};
@@ -159,7 +160,19 @@ if ($organism eq "human") {
$array[9] =~ s/\'/\\\'/g;
print OUT "$array[1]\tSPTR\t$array[4]\tGO\t$array[4]\t$array[9]\tXREF\n";
}
+
+ close (GO);
+
+#Get the GKB (Genome Knowledge Database) mapping
+#Contacts: Imre Vastrik <vastrik@ebi.ac.uk>, Hester <eschmidt@ebi.ac.uk>
+ open (GKB,"$gkb") || die "Can't open GKB data: $gkb";
+
+ while (<GKB>) {
+ chomp;
+ my ($sp,$id) = split;
+ print OUT "$sp\tSPTR\t$id\tGKB\t$id\t\tXREF\n";
+ }
}
#Get Xref mapping specifically for mouse.
@@ -302,6 +315,7 @@ if($organism eq 'briggsae'){
close(OUT);
print STDERR "The output has been written there: $out\n";
+
sub parse_sp_file{
my ($file) = @_;
#print STDERR "opening file ".$file."\n";
@@ -473,3 +487,4 @@ sub process_parsed_sp{
}
}
}
+
diff --git a/misc-scripts/protein_match/mapping_conf.pl b/misc-scripts/protein_match/mapping_conf.pl
index 41f00ab97f..2a3dc067e7 100644
--- a/misc-scripts/protein_match/mapping_conf.pl
+++ b/misc-scripts/protein_match/mapping_conf.pl
@@ -104,6 +104,11 @@ package main;
#ftp.ebi.ac.uk/pub/databases/GO/goa/HUMAN/gene_association.goa_human.gz
#'go' => '',
'go' => '',
+
+ #Location of the file for GKB (Genome Knowledge Base) mapping.
+ #Contacts: Imre Vastrik <vastrik@ebi.ac.uk>, Hester <eschmidt@ebi.ac.uk>
+
+ 'gkb' => '',
#######
#Mouse#
diff --git a/misc-scripts/protein_match/maps2db.pl b/misc-scripts/protein_match/maps2db.pl
index a6f4693d64..6742085563 100644
--- a/misc-scripts/protein_match/maps2db.pl
+++ b/misc-scripts/protein_match/maps2db.pl
@@ -355,13 +355,7 @@ if ($organism eq "drosophila") {
}
-if ($organism eq "drosophila") {
- my $query = "select distinct(stable_id) from gene_stable_id";
- my $sth = $db->prepare($query);
-
-
-}
if ($organism eq "elegans") {
#print STDERR " parsing wormbase information\n";
--
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