From 510c79b670474f4f899da5169d99acc2412c0a9b Mon Sep 17 00:00:00 2001
From: elserj <elserj@localhost>
Date: Tue, 21 Sep 2010 21:10:52 +0000
Subject: [PATCH] Modified to take input and output files as arguments (better
 for scripting)

svn path=/; revision=41
---
 interactome_scripts/fasta_header_fix.pl | 36 +++++++++++--------------
 1 file changed, 16 insertions(+), 20 deletions(-)

diff --git a/interactome_scripts/fasta_header_fix.pl b/interactome_scripts/fasta_header_fix.pl
index eaaa1a8..f20fce6 100755
--- a/interactome_scripts/fasta_header_fix.pl
+++ b/interactome_scripts/fasta_header_fix.pl
@@ -7,29 +7,25 @@ require "$ENV{HOME}/scripts/jaiswallab/interactome_scripts/find_species.pl";
 
 my @files;
 
-if($#ARGV == 0) {
-	@files = $ARGV[0];
-}else{
-	@files = glob("*.fa");
+if($#ARGV == 1) {
+	$input_file = $ARGV[0];
+	$output_file = $ARGV[1];
 }
 
-foreach my $input_file (@files) {
-	open(in_file, $input_file)  || die "Error: File $input_file can not be opened";
-	my $output_file = $input_file . "_fixed.fa";
-	open(out_file, ">$output_file");
+open(in_file, $input_file)  || die "Error: File $input_file can not be opened";
+open(out_file, ">$output_file");
 	
-	my $species = find_species($input_file);
+my $species = find_species($input_file);
 
-	while(<in_file>) {
-		my $line = $_;
-		chomp $line;
-		if ($line =~ /^>/) {
-			my $gene = find_gene($line,$species);
-			$line = ">" . "$gene";
-		}
-		print out_file "$line\n";
+while(<in_file>) {
+	my $line = $_;
+	chomp $line;
+	if ($line =~ /^>/) {
+		my $gene = find_gene($line,$species);
+		$line = ">" . "$gene";
 	}
-
-	close(in_file);
-	close(out_file);
+	print out_file "$line\n";
 }
+
+close(in_file);
+close(out_file);}
-- 
2.34.1