Modified to take input and output files as arguments (better for scripting)

svn path=/; revision=41

diff --git a/interactome_scripts/fasta_header_fix.pl b/interactome_scripts/fasta_header_fix.pl
index eaaa1a8ecb21ff476cf877a9a987311a5a1e1f00..f20fce6cb5b730486ed383543b9994917524a4a1 100755 (executable)
--- 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);}