Use subroutine to get species array and cleaned up unused code

svn path=/; revision=40

diff --git a/interactome_scripts/supercluster.pl b/interactome_scripts/supercluster.pl
index bef30d95615e042897c3af6c6a8b6913fa8b00f0..66439a986d296cdc9c2c1195382d47bf8956622b 100755 (executable)
--- a/interactome_scripts/supercluster.pl
+++ b/interactome_scripts/supercluster.pl
@@ -25,6 +25,7 @@ use strict;
 use DBI;
 use Term::Screen::ReadLine;
 
+require "$ENV{HOME}/scripts/jaiswallab/interactome_scripts/find_species.pl";
 
 # define the database handle to be used 
 
@@ -72,22 +73,14 @@ $dbh->do("CREATE TABLE $safe_super_table (
        ) TYPE = MYISAM");
        
        
-#$dbh->do("CREATE TABLE $safe_super_table (
-#      `super_id` INT( 11 ) NOT NULL ,
-#      `gene` VARCHAR( 255 ) NOT NULL ,
-#      UNIQUE ( `gene` )
-#      ) TYPE = MYISAM");
-       
 my $insert_sth = $dbh->prepare("insert ignore into $safe_super_table (super_id, species, gene) values (?,?,?)");
-#my $insert_sth = $dbh->prepare("insert ignore into $safe_super_table (super_id, gene) values (?,?)");
 
 my $super_id = 0; #initialize the super cluster id
 my %super_hash;
 my %big_count_hash;
        
-#my @species = ("Ath", "Brachy", "Maize", "Oryza_sativa", "Sorghum");
-my @species = ("Ath", "Fragaria", "Oryza_sativa", "Vitis");
-#my @species  = ("Ath", "Brachy", "C_elegans", "Chlamy", "Danio", "E_coli", "Fragaria", "Glycine", "Human", "Maize", "Mouse", "Neurospora", "Oryza_sativa", "Physcomitreall", "Poplar", "Sacc_cerevisiae", "Sacc_pombe", "Selaginella", "Sorghum", "Synechosystis", "Vitis");
+#my @species  = ("Ath", "Brachy", "C_elegans", "Chlamy", "Danio", "E_coli", "Fragaria", "Glycine", "Human", "Maize", "Mouse", "Neurospora", "Oryza_sativa", "Physcomitreall", "Poplar", "P_persica", "Sacc_cerevisiae", "Sacc_pombe", "Selaginella", "Sorghum", "Synechosystis", "Vitis");
+my @species = all_species_array();
 my $num_species = @species;
 
 for (my $i=0; $i<$num_species-1; $i++) {
@@ -100,15 +93,15 @@ for (my $i=0; $i<$num_species-1; $i++) {
                #    Confirmed with no output from print statement.
                my $species_1 = $species[$i];
                my $species_2 = $species[$j];
-               if ($species_1 lt $species_2) {
-                       $species_1 = $species_1;
-                       $species_2 = $species_2;
-               } else {
-                       my $spec_temp = $species_1;
-                       $species_1 = $species_2;
-                       $species_2 = $spec_temp;
-                       print "non optimal order\n";
-               }
+       #       if ($species_1 lt $species_2) {
+       #               $species_1 = $species_1;
+       #               $species_2 = $species_2;
+       #       } else {
+       #               my $spec_temp = $species_1;
+       #               $species_1 = $species_2;
+       #               $species_2 = $spec_temp;
+       #               print "non optimal order\n";
+       #       }