Small path fixes + remove most stderr debug outputs

Exonerate.pm

@@ -57,7 +57,7 @@ sub parser{
         }
     }
     close $MAP;
-    print "[@cdsUp]\n" if ( $debug );
+    print {*STDERR} "[@cdsUp]\n" if ( $debug );
 
 
     my $drap     = 0;
@@ -72,11 +72,11 @@ sub parser{
         if ( $drap==3 && $matched_symbol =~ /^[\+\-]$/ ){
             $drap  = 0;
             $locus = 0;
-            print $matched_symbol, substr($Genom, $i, 1), "\t", substr($Query, $i, 1), "\n" if ($debug);
+            print {*STDERR} $matched_symbol, substr($Genom, $i, 1), "\t", substr($Query, $i, 1), "\n" if ($debug);
         }
         elsif ( $matched_symbol =~ /^[\+\-]$/ ){
             $drap++;
-            print $matched_symbol, substr($Genom, $i, 1), "\t", substr($Query, $i, 1), "\n" if ($debug);
+            print {*STDERR} $matched_symbol, substr($Genom, $i, 1), "\t", substr($Query, $i, 1), "\n" if ($debug);
         }
 #       elsif ( $matched_symbol =~ /[ \|\.\!\:]/ && substr($Genom,$i,1) !~ /[\{\}\.a-z\-]/ ){
         elsif ( $matched_symbol =~ /[ \|\.\!\:\#]/ && substr($Genom, $i, 1) !~ /[\{\}\.a-z]/ ){
@@ -108,16 +108,16 @@ sub parser{
             }
             my $shift = '';
             $shift    = "\t$frameIntron" if ( $frameIntron>0 );
-            print $line, "$shift\n" if ($debug);
+            print {*STDERR} $line, "$shift\n" if ($debug);
             $locus++;
         }
         elsif ( $matched_symbol =~ /\{/ ){
-            print $matched_symbol, substr($Genom, $i, 1), "\t", substr($Query, $i, 1), "\n" if ($debug);
+            print {*STDERR} $matched_symbol, substr($Genom, $i, 1), "\t", substr($Query, $i, 1), "\n" if ($debug);
             $frameIntron = -1;
             $accolade++;
         }
         else{
-            print $matched_symbol, substr($Genom, $i, 1), "\t", substr($Query, $i, 1), "\n" if ($debug);
+            print {*STDERR} $matched_symbol, substr($Genom, $i, 1), "\t", substr($Query, $i, 1), "\n" if ($debug);
             $lieu++ if ( substr($Query, $i, 1) =~ /U/ );
             if ( substr($Query, $i, 1) =~ /\}/ ){
                 if ( $frameIntron==1 ){

Views.pm

@@ -68,7 +68,7 @@ sub Html {
 
     open (my $CDSP,    '<', "$file")      or die "\tCannot open '$file'\n";
     open (my $CDSHTML, '>', "$file.html") or die "\tCannot create in '$file.html'\n";
-    print {$CDSHTML} &htmlHeader($file);
+    print {$CDSHTML} htmlHeader($file);
     {
         my $isOdd    = 'odd';
         my $isSubOdd = 'odd';
@@ -162,7 +162,7 @@ sub Html {
 
 sub htmlHeader {
     my ($jobName) = @_;
-    $jobName =~ s{^.*/([^\/]+?)\.cdsP$}{$1};    
+    $jobName =~ s{^.*?([^\/]+?)\.cdsP$}{$1};    
 
     my $css = '';
     for my $style ( keys(%css) ){

Views0.pm

@@ -198,7 +198,7 @@ sub Html {
 
     open (my $CDSP,    '<', "$file")      or die "\tCannot open '$file'\n";
     open (my $CDSHTML, '>', "$file.html") or die "\tCannot create in '$file.html'\n";
-    print {$CDSHTML} &htmlHeader($file);
+    print {$CDSHTML} htmlHeader($file);
     {
         my $isOdd    = 'odd';
         my $isSubOdd = 'odd';
@@ -329,7 +329,7 @@ sub Html {
 
 sub htmlHeader {
     my ($jobName) = @_;
-    $jobName =~ s{^.*/([^\/]+?)\.cdsP$}{$1};    
+    $jobName =~ s{^.*?([^\/]+?)\.cdsP$}{$1};    
 
     my $css = '';
     for my $style ( keys(%css) ){