From: elserj <elserj@localhost>
Date: Fri, 28 Jun 2013 23:41:08 +0000 (+0000)
Subject: Now needs a supplied species list file.  No longer needs to be manually edited to... 
X-Git-Url: http://gitweb.planteome.org/?a=commitdiff_plain;h=d02c35aa95addddd62a19615d09ad2fadce6a5e3;p=old-jaiswallab-svn%2F.git

Now needs a supplied species list file.  No longer needs to be manually edited to enter species names

svn path=/; revision=490
---

diff --git a/interactome_scripts/supercluster.pl b/interactome_scripts/supercluster.pl
index d30dbef..df5f2a0 100755
--- a/interactome_scripts/supercluster.pl
+++ b/interactome_scripts/supercluster.pl
@@ -35,6 +35,14 @@ if(-e "$ENV{HOME}/scripts/jaiswallab/interactome_scripts/find_species.pl") {
 	require "$ENV{HOME}/bin/find_species.pl";
 }
 
+# check for arguments and explain usage
+if ($#ARGV !=0) {
+	print "usage: supercluster.pl species_list_file\n";
+	exit;
+}
+
+my $spec_file = $ARGV[0];
+
 my $dbh = DbiFloret::dbconnect;
 	
 print "Minimum paralogy score: ";
@@ -44,7 +52,16 @@ if($min_score eq "") {
 	$min_score = 0;
 }
 
-	
+my @species;
+
+open(SPECFILE, "$spec_file");
+
+while(<SPECFILE>) {
+		my $line = $_;
+		chomp $line;
+		push (@species, $line);
+}
+
 	
 #### Note to self ####
 ## To not have multiple values in mysql table, use insert ignore instead of insert.  Or use replace.
@@ -69,8 +86,6 @@ my $super_id = 0; #initialize the super cluster id
 my %super_hash;
 my %big_count_hash;
 	
-my @species  = ("Arabidopsis_lyrata", "Arabidopsis_thaliana", "Carica_papaya", "Citrus_clementina", "Citrus_sinensis", "Eucalyptus_grandis", "Fragaria_vesca", "Malus_domestica", "Oryza_sativa", "Populus_trichocarpa", "Prunus_persica", "Vitis_vinifera");
-#my @species = all_species_array();
 my $num_species = @species;
 
 for (my $i=0; $i<$num_species-1; $i++) {