quick test for missing files from mapping

misc-scripts/xref_mapping/test_mapping_files.pl

+use strict;
+use warnings;
+
+my $dir = shift;
+
+opendir(DIR, $dir);
+my @allfiles = readdir DIR;
+closedir DIR;
+
+#xref_0_dna.3100129-307.out
+#ExonerateGappedBest1_dna_307.map
+#xref_0_dna.3100129-307.err
+
+my %hash;
+my %max;
+
+foreach my $file(@allfiles){
+  if($file eq '.' || $file eq '..'){
+    next;
+  }elsif(-d $file){
+    next;
+  }else{
+    my $type;
+    if($file =~ /dna/){
+      $type = 'dna';
+    }
+    elsif($file =~ /pep/){
+      $type = 'pep';
+    }
+    elsif($file =~ /fasta/){
+      next;
+    }
+    else{
+      next;
+    }
+    if($file =~ /_(\d+).map/){
+      $hash{$type}{'map'}{$1} = $1;
+    }
+    elsif($file =~ /-(\d+).err/){
+      if($max{$type} < $1){
+	$max{$type} = $1
+      }
+      $hash{$type}{'err'}{$1} = $1;
+    }
+    elsif($file =~ /-(\d+).out/){
+      $hash{$type}{'out'}{$1} = $1;
+    }
+  }
+}
+
+
+foreach my $type ('pep', 'dna'){
+  print "max ".$type."-->".$max{$type}."\n";
+  for (my $i=1; $i <= $max{$type}; $i++){
+    if(!defined($hash{$type}{'map'}{$i})){
+      print $i,".map\n";
+    }
+    if(!defined($hash{$type}{'err'}{$i})){
+      print $i,".err\n";
+    }
+    if(!defined($hash{$type}{'out'}{$i})){
+      print $i,".out\n";
+    }
+  }
+}