Fixes the gene headers in the fasta files so that they are correctly parsed by blast...

svn path=/; revision=37

diff --git a/interactome_scripts/fasta_header_fix.pl b/interactome_scripts/fasta_header_fix.pl
new file mode 100755 (executable)
index 0000000..eaaa1a8
--- /dev/null
+++ b/interactome_scripts/fasta_header_fix.pl
@@ -0,0 +1,35 @@
+#!/usr/bin/perl
+
+use strict;
+use warnings;
+
+require "$ENV{HOME}/scripts/jaiswallab/interactome_scripts/find_species.pl";
+
+my @files;
+
+if($#ARGV == 0) {
+       @files = $ARGV[0];
+}else{
+       @files = glob("*.fa");
+}
+
+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");
+       
+       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";
+       }
+
+       close(in_file);
+       close(out_file);
+}