diff gomwu_a.pl @ 2:5acf9dfdfa27 draft default tip

planemo upload commit 66a856bcce69986d9a6f1a39820dd9b3f4f6b0db

--- a/gomwu_a.pl	Tue Apr 19 08:28:43 2022 +0000
+++ b/gomwu_a.pl	Wed Nov 09 08:57:54 2022 +0000
@@ -287,53 +287,53 @@
 
 ################################
 
-	#warn "comparing categories...\n"; 
+#warn "comparing categories...\n"; 
 #my $clfile="cl_".$inname31;
 #if($dones!~/ $clfile /) { 
 
-	use List::Util qw[min max];
-	for ($g1=0;$g1<=$#gos;$g1++){
-		my $go=@gos[$g1];
-		next if ($gonego{$go}==1);
-	#warn "----------------\n$go  $desc{$go}  level $level{$go}\n";
-		my $goos=$go;
-		my $lev=$level{$go};
-		my $dsc=$desc{$go};
-		for ($g2=$g1+1;$g2<=$#gos;$g2++){
-			my $go2=@gos[$g2];	
-			next if ($gonego{$go2}==1);
-			next if ($ggi{$go2}==1);
-			my %seen={}; 
-			my $count=0;
-			my @combo=();
-			if ($lump<=1) {
-				foreach $g (@{$genes{$go}},@{$genes{$go2}}){
-					unless($seen{$g}==1 ){
-						$count++;
-						$seen{$g}=1;
-						push @combo, $g;
-					}
-				}
-				my $shared=$#{$genes{$go}}+1+$#{$genes{$go2}}+1-$count;
-				$overlap{$go,$go2}=min($shared/($#{$genes{$go}}+1),$shared/($#{$genes{$go2}}+1));			
-				$overlap{$go2,$go}=min($shared/($#{$genes{$go}}+1),$shared/($#{$genes{$go2}}+1));			
-			}
-		}
-	}
+use List::Util qw[min max];
+for ($g1=0;$g1<=$#gos;$g1++){
+    my $go=@gos[$g1];
+    next if ($gonego{$go}==1);
+    #warn "----------------\n$go  $desc{$go}  level $level{$go}\n";
+    my $goos=$go;
+    my $lev=$level{$go};
+    my $dsc=$desc{$go};
+    for ($g2=$g1+1;$g2<=$#gos;$g2++){
+        my $go2=@gos[$g2];	
+        next if ($gonego{$go2}==1);
+        next if ($ggi{$go2}==1);
+        my %seen={}; 
+        my $count=0;
+        my @combo=();
+        if ($lump<=1) {
+            foreach $g (@{$genes{$go}},@{$genes{$go2}}){
+                unless($seen{$g}==1 ){
+                    $count++;
+                    $seen{$g}=1;
+                    push @combo, $g;
+                }
+            }
+            my $shared=$#{$genes{$go}}+1+$#{$genes{$go2}}+1-$count;
+            $overlap{$go,$go2}=min($shared/($#{$genes{$go}}+1),$shared/($#{$genes{$go2}}+1));			
+            $overlap{$go2,$go}=min($shared/($#{$genes{$go}}+1),$shared/($#{$genes{$go2}}+1));			
+        }
+    }
+}
 
-	open OUT, ">$inname31" or die "gomwu_a: cannot create output $inname31\n";
-	
-	print {OUT} join("\t",@gos),"\n";
+open OUT, ">$inname31" or die "gomwu_a: cannot create output $inname31\n";
+
+print {OUT} join("\t",@gos),"\n";
 
-	foreach $go (@gos) {
-		$overlap{$go,$go}=1;
-		foreach $go2 (@gos){
-			print {OUT} sprintf("%.3f",1-$overlap{$go,$go2});;
-			print {OUT} "\t" unless ($go2 eq $gos[$#gos]);
-		}
-		print {OUT} "\n";
-	}
-	close OUT;
+foreach $go (@gos) {
+    $overlap{$go,$go}=1;
+    foreach $go2 (@gos){
+        print {OUT} sprintf("%.3f",1-$overlap{$go,$go2});;
+        print {OUT} "\t" unless ($go2 eq $gos[$#gos]);
+    }
+    print {OUT} "\n";
+}
+close OUT;
 #}
 
 #print "calling clusteringGOs.R script ....\n";