Script to run TARGETP Aplication

svn path=/; revision=206

diff --git a/interpro/RUN_TARGETP.pl b/interpro/RUN_TARGETP.pl
index 2c83d0dfc221d87633c234e2e895dad5e4ea0ba0..c61f799246cb33207a09d02758acaca872be31a8 100644 (file)
--- a/interpro/RUN_TARGETP.pl
+++ b/interpro/RUN_TARGETP.pl
@@ -1,15 +1,27 @@
 #!/usr/bin/perl
-#use strict;
-# create the variables
-# keys is $gene_header, values is $seq
+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 $saeq;
-$file = "/lemma/Rajani/iprscan/Toly_new.fa";   
+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;
 
@@ -22,30 +34,29 @@ while(<in_file>)
              }
                   $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";
-#}
+    }
+# 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";
+     while (($key, $value) = each(%seq_hash))
+       {
+             # print $key."\n".$value."\n";
 
-              open(FILE1,">Toly.fa") || die("Cannot Open File");
+              open(FILE1,">species_targetp.seq") || die("Cannot Open File");
               print FILE1 "$key\n";
               print FILE1 "$value";
+              $status = system("/lemma/SignalP/targetp-1.1/targetp -P /lemma/Rajani/iprscan/species_targetp.seq >> targetp_species.out");
 
-$astatus6 = system("/lemma/SignalP/targetp-1.1/targetp -P /lemma/Rajani/iprscan/Toly.fa >> targetp_4_Toly.out");
-
-}
+       }