From 3c3350a6d4b31aa41a1430c30ca5fb5af72c31cc Mon Sep 17 00:00:00 2001
From: Tim Hubbard <th@sanger.ac.uk>
Date: Sun, 22 Feb 2004 10:16:40 +0000
Subject: [PATCH] MGI file changes
---
misc-scripts/protein_match/get_Xmapping.pl | 20 +++++++++----------
.../protein_match/mapping_conf.pl.example | 5 +++--
2 files changed, 13 insertions(+), 12 deletions(-)
diff --git a/misc-scripts/protein_match/get_Xmapping.pl b/misc-scripts/protein_match/get_Xmapping.pl
index e46fc41a2d..8442eabf14 100644
--- a/misc-scripts/protein_match/get_Xmapping.pl
+++ b/misc-scripts/protein_match/get_Xmapping.pl
@@ -321,17 +321,17 @@ if ($organism eq "human") {
#Get Xref mapping specifically for mouse.
if ($organism eq "mouse") {
my %mgi2sp;
+ # 20/02/04:th MGI changed files for MGI to SP mappings. File format also changed
+ # moving $sps from 6th to 7th column.
open (MGISP, "$mgi_sp") || die "Can't open $mgi_sp\n";
while (<MGISP>) {
- chomp;
- my ($mgi,$rik,$a,$b,$c,$sps) = split (/\t/,$_);
-
- my @sp = split(/\s/,$sps);
-
- #put in hash all of the SP entries which correspond to an MGI (this will be used later)
- $mgi2sp{$mgi} = $sps;
-
+ chomp;
+ my ($mgi,$rik,$a,$b,$c,$d,$sps) = split (/\t/,$_);
+ my @sp = split(/\s/,$sps);
+ #put in hash all of the SP entries which correspond to an MGI (this will be used later)
+ $mgi2sp{$mgi} = $sps;
}
+ close MGISP;
open (MGILOC, "$mgi_locus") || die "Can't open $mgi_locus\n";
my %mgi_got;
my %mgi_syns;
@@ -348,9 +348,9 @@ if ($organism eq "mouse") {
}
}else{
$mgi_got{$mgi} = $locus;
- }
-
+ }
}
+ close MGILOC;
my @mgi_ids = keys(%mgi_got);
foreach my $mgi(@mgi_ids){
diff --git a/misc-scripts/protein_match/mapping_conf.pl.example b/misc-scripts/protein_match/mapping_conf.pl.example
index ca100d475d..83b6c45382 100644
--- a/misc-scripts/protein_match/mapping_conf.pl.example
+++ b/misc-scripts/protein_match/mapping_conf.pl.example
@@ -122,8 +122,9 @@ package main;
#The files needed for the mouse X_mapping can be obatained there: ftp://ftp.informatics.jax.org/pub/reports/
#2 files are needed MRK_SwissProt.rpt and MRK_LocusLink.rpt
- #File containing MGI/SP mapping (MRK_SwissProt.rpt)
- #'mgi_sp' => '/work1/mongin/mouse/mapping/primary/MRK_SwissProt.rpt',
+ #File containing MGI/SP mapping (MRK_SwissProt_TrEMBL.rpt)
+ #(20/02/04:th: file format changed, so get_Xmapping.pl changed at this point)
+ #'mgi_sp' => '/work1/mongin/mouse/mapping/primary/MRK_SwissProt_TrEMBL.rpt',
'mgi_sp' => '',
#File containing MGI/LocusLink mapping (MRK_LocusLink.rpt)
--
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