From: elserj <elserj@localhost>
Date: Mon, 27 Sep 2010 23:25:38 +0000 (+0000)
Subject: Added detection of non-unique gene-ids
X-Git-Url: http://gitweb.planteome.org/?a=commitdiff_plain;h=4a14b9dec3ba4929bd5bc502f5d08e518c059259;p=old-jaiswallab-svn%2F.git

Added detection of non-unique gene-ids

svn path=/; revision=52
---

diff --git a/interactome_scripts/fasta_verify.pl b/interactome_scripts/fasta_verify.pl
index 6f12a38..ac6eb84 100755
--- a/interactome_scripts/fasta_verify.pl
+++ b/interactome_scripts/fasta_verify.pl
@@ -3,20 +3,26 @@
 use strict;
 use warnings;
 
+require "$ENV{HOME}/scripts/jaiswallab/interactome_scripts/find_species.pl";
+
 
 if($#ARGV != 0) {
-	print "usage: fasta_verify.pl fast_file\n";
+	print "usage: fasta_verify.pl fasta_file\n";
 	exit;
 }
 
 my $in_file = $ARGV[0];
 
+my $species = find_species($in_file);
+
 open(in_file, "$in_file");
 
 my $prev_line_is_header = 0;
 
 my $counter = 0;
 
+my %gene_id_hash;
+
 while(<in_file>) {
 	my $line = $_;
 	chomp $line;
@@ -46,6 +52,13 @@ while(<in_file>) {
 	# set prev_line_header info for next time through loop
 	if($curr_line_is_header) {
 		$prev_line_is_header = 1;
+		#my $gene = find_gene($line,$species);
+		my $gene = $line;
+		if(!defined($gene_id_hash{$gene})) {
+			$gene_id_hash{$gene} = $line;
+		}else{
+			print "Error: gene $gene has multiple sequences associated with it in file $in_file\n"
+		}
 	}else{
 		$prev_line_is_header = 0;
 	}