Script to run TMMHMM

svn path=/; revision=201

diff --git a/interpro/.gitignore b/interpro/.gitignore
deleted file mode 100644 (file)
index e69de29..0000000

diff --git a/interpro/RUN_TMHMM.pl b/interpro/RUN_TMHMM.pl
new file mode 100644 (file)
index 0000000..6aaf9a2
--- /dev/null
+++ b/interpro/RUN_TMHMM.pl
@@ -0,0 +1,52 @@
+#!/usr/bin/perl
+#use strict;
+# create the variables
+# keys is $gene_header, values is $seq
+my %seq_hash; 
+my $gene_header;
+my $saeq;
+$file = "/lemma/Rajani/iprscan/Toly_new.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;
+
+       }
+   
+#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,">Toly.seq") || die("Cannot Open File");
+              print FILE1 "$key\n";
+              print FILE1 "$value";
+
+$status7 = system("/lemma/SignalP/TMHMM2.0c/bin/tmhmm  tmhmm Toly.seq >> Toly_tmhmmdata.txt");
+
+
+}
+
+