Fix the species printing in output to not have underscore "_"

svn path=/; revision=679

diff --git a/interactome_scripts/cafe_from_inparanoid.pl b/interactome_scripts/cafe_from_inparanoid.pl
index 5c2ab45ac660046547d03ced7bbbe83a00711c3c..9ccca41dd662907c56a2dc7978929f3563e15aa5 100755 (executable)
--- a/interactome_scripts/cafe_from_inparanoid.pl
+++ b/interactome_scripts/cafe_from_inparanoid.pl
@@ -25,6 +25,8 @@ my $dbh = DbiFloret::dbconnect;
 my $in_file = $ARGV[0];
 my $out_file = $ARGV[1];
 
+my $max_genes = 100;
+
 # Get list of species to check
 my @species_list;
 
@@ -71,7 +73,9 @@ open(OUTFILE, ">$out_file");
 print OUTFILE "Description\tID";
 # Print species list to output file
 for my $species (@species_list) {
-               print OUTFILE "\t$species";
+       my $species_sub = $species;
+       $species_sub =~ s/_//;
+       print OUTFILE "\t$species_sub";
 }
 print OUTFILE "\n";
 
@@ -98,13 +102,17 @@ for my $super_id (sort {$a <=> $b} keys %cluster_hash) {
                # drop any lines (clusters) that only have one species in them
                my @line_array = split("\t", $mid_line);
                my @match_array;
+               my $max_over = 1;
                foreach my $elem (@line_array) {
                                if($elem != 0) {
                                                push(@match_array, $elem);
                                }
+                               if($elem >=  $max_genes) {
+                                       $max_over = 0;
+                               }
                }
                my $match_count = @match_array;
-               if ($match_count != 1) {
+               if ($match_count != 1 && $max_over) {
                                print OUTFILE "$super_id\t$super_id\t$mid_line\n";
                }
 }