From a23fa08c01d72d848fc0b552c85e01f448480358 Mon Sep 17 00:00:00 2001
From: rajar <rajar@localhost>
Date: Wed, 2 Nov 2011 21:42:55 +0000
Subject: [PATCH] Script to run TMHMM application

svn path=/; revision=210
---
 interpro/RUN_TMHMM.pl | 66 +++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 66 insertions(+)
 create mode 100644 interpro/RUN_TMHMM.pl

diff --git a/interpro/RUN_TMHMM.pl b/interpro/RUN_TMHMM.pl
new file mode 100644
index 0000000..465999b
--- /dev/null
+++ b/interpro/RUN_TMHMM.pl
@@ -0,0 +1,66 @@
+#!/usr/bin/perl
+   use strict;
+   use warnings;
+
+####################################################################################
+# create the variables                                                             #
+# keys is $gene_header, values is $seq                                             #
+# Just replace the word species in this file with the species that you are working.#
+# species word appears 4 times in this file.                                       #
+####################################################################################
+
+my %seq_hash; 
+my $gene_header;
+my $seq;
+my $file;
+my $key;
+my $value;
+my $status;
+
+$file = "/lemma/Rajani/iprscan/species.fa";   
+open(in_file,$file);
+   
+   while(<in_file>) 
+     {
+        my $line = $_;
+        chomp $line;
+
+
+        if($line =~ /^\>/)
+          {
+               if(defined($gene_header))
+             {
+                  $seq_hash{$gene_header} = $seq;
+             }
+                  $gene_header = $line;
+                  $seq = "";
+         }
+        else
+             {
+                  $seq = "$seq"."$line";
+             }
+            $seq_hash{$gene_header} = $seq;
+
+    }
+# To display the keys and values  on the screen    
+#     foreach $key(%seq_hash)
+#      {
+#          print "Gene is $key  and the sequence is  $seq_hash{$gene_header} \n";
+#      }
+
+
+
+           while (($key, $value) = each(%seq_hash))
+            {
+                # print $key."\n".$value."\n";
+
+                open(FILE1,">species.seq") || die("Cannot Open File");
+                print FILE1 "$key\n";
+                print FILE1 "$value";
+
+                $status = system("/lemma/SignalP/TMHMM2.0c/bin/tmhmm  tmhmm species.seq >> species_tmhmmdata.txt");
+
+
+            }
+
+
-- 
2.34.1