Generalize it to take in species_array from a file so the program doesn't need to...

svn path=/; revision=676

diff --git a/interactome_scripts/create_venn_diagram.pl b/interactome_scripts/create_venn_diagram.pl
index 092debbd798029a370d33d0d0e9e0e84d15b7902..6e19896ee08b8ee5eca8ed062e855ffdfe6b0b75 100755 (executable)
--- a/interactome_scripts/create_venn_diagram.pl
+++ b/interactome_scripts/create_venn_diagram.pl
@@ -11,6 +11,11 @@ use lib "$ENV{HOME}/scripts/jaiswallab/interactome_scripts";
 
 my $venn_src_dir = "$ENV{HOME}/jaiswallab_svn/Personnel/elserj/venn_sources";
 
+if($#ARGV != 0) {
+       print "Usage: create_venn_diagram.pl species_list_file\n";
+       exit;
+}
+
 use DbiFloret;
 
 print "User credentials for the supercluster database\n";
@@ -21,14 +26,25 @@ my $dbh = DbiFloret::dbconnect;
 print "User credentials for the protein sequences database\n";
 my $dbh_seq = DbiFloret::dbconnect;
 
+# read species from file
+my @species_array;
+my $infile = $ARGV[0];
+open(INFILE, $infile)  || die "Error: File $infile can not be opened";
+while(<INFILE>) {
+       my $line = $_;
+       chomp $line;
+       push(@species_array, $line);
+}
+close(INFILE);
+
 # human_mouse_kangaroo_rat_platypus_beaver
-my @species_array = ("Arabidopsis_thaliana", "Cannabis_sativa.CRBRx", "Humulus_lupulus.primary", "Salvia_hispanica", "Vitis_vinifera");
+#my @species_array = ("Arabidopsis_thaliana", "Cannabis_sativa.CRBRx", "Humulus_lupulus.haplotig", "Humulus_lupulus.primary", "Vitis_vinifera");
 # beaver_human_mouse_rat_platypus
 #my @species_array = ("Castor_canadensis.brent.proteins", "Homo_sapiens", "Mus_musculus", "Ornithorhynchus_anatinus", "Rattus_norvegicus");
 # human_mouse_beaver_rabbit_ferret
 #my @species_array = ("Castor_canadensis.brent.proteins", "Homo_sapiens", "Mus_musculus", "Mustela_putorius.furo" , "Oryctolagus_cuniculus");
 #my @species_array = ("Aegilops_tauschii", "Hordeum_vulgare", "TmDV92", "TmG3116");
-#my @species_array = ("Aegilops_tauschii", "Hordeum_vulgare", "TmDV92");
+#my @species_array = ("Arabidopsis_thaliana", "Homo_sapiens", "Oryza_sativa.japonica.IRGSP");
 my $species_array_size = @species_array;
 
 my %gene_hash;