From cf935ca1badc0fa0e7912d2d9e1e9e46aa24bca8 Mon Sep 17 00:00:00 2001
From: preecej <preecej@localhost>
Date: Thu, 2 Jan 2014 23:04:34 +0000
Subject: [PATCH] swaps the GBWI ids w/ GRMZ ids for Gramene web site indexing

svn path=/; revision=518
---
 .../gramene/maizecyc_GRMZ_GBWI_swap.pl        | 38 +++++++++++++++++++
 1 file changed, 38 insertions(+)
 create mode 100644 Personnel/preecej/perl_singletons/gramene/maizecyc_GRMZ_GBWI_swap.pl

diff --git a/Personnel/preecej/perl_singletons/gramene/maizecyc_GRMZ_GBWI_swap.pl b/Personnel/preecej/perl_singletons/gramene/maizecyc_GRMZ_GBWI_swap.pl
new file mode 100644
index 0000000..2747acf
--- /dev/null
+++ b/Personnel/preecej/perl_singletons/gramene/maizecyc_GRMZ_GBWI_swap.pl
@@ -0,0 +1,38 @@
+#!/usr/bin/perl -w
+use strict;
+
+my $map_file = $ARGV[0]; #GBWI::GRMZ mapping file
+
+# # cyc pathway dump file (generated w/ brie:/usr/local/gramene/gramene-lib/scripts/pathway/format-pathway-data.pl (see README for conventional usage))
+my $dump_file = $ARGV[1]; 
+my %map_hash;
+
+open(MAP_FILE,$map_file) or die("could not open $map_file");
+while (<MAP_FILE>)
+{
+    my $line = $_;
+    chomp $line;
+    my @line_ary = split('\t',$line);
+    my $key = $line_ary[0];
+    $key =~ s/\s+$//;
+    my $val = $line_ary[1];
+    $val =~ s/^\s+//;
+    
+    $map_hash{$key} = $val;
+}
+close(MAP_FILE);
+
+open(DUMP_FILE,$dump_file) or die("could not open $dump_file");
+while (<DUMP_FILE>)
+{
+    my $line = $_;
+    chomp $line;
+    my @line_ary = split('\t',$line);
+    
+    if ($map_hash{$line_ary[0]}) {
+        print $map_hash{$line_ary[0]} . "\t" . $line_ary[1] . "\t" . $line_ary[2] . "\t" 
+            . $line_ary[3] . "\t" . $line_ary[4] . "\t" . $line_ary[5] . "\t" . $line_ary[6] . "\n";
+    }
+}
+close(DUMP_FILE);
+
-- 
2.34.1