fixed for new style contigs IDs

moved sub's to bottom to make it readable

misc-scripts/golden_path/gp_contig_mismatch.pl

@@ -20,89 +20,12 @@ print STDERR ( "Start reading contig.txt.\n" );
 
 while( <CF> ) {
   my ( $contig, $offset, $length  ) = split;
-  ( $clone ) = $contig =~ /^([^\.]+)\./;
+  ( $clone ) = $contig =~ /^([^\.]+\.\d+)\./;
   $clone_offset_hash{$clone}->{$contig} = [ $offset, $length ];
 }
 close CF;
 
 print STDERR ( "Contig.txt read.\n" );
- 
-sub append_agp {
-  /\.agp$/ &&
-    push( @filelist, $File::Find::name );
-}
-
-sub read_agp {
-  $filename = shift;
-  local *FH;
-  open( FH, $filename ) or die( "Cant open file $filename." );
-  
-  while( <FH> ) {
-    /^#/ && next;
-    @list = split( /\t/, $_ );
-    if( $list[4] =~ /[^N]/ ) {
-      $readLines++;
-      ( $clone ) = $list[5] =~ /^([^\.]+)\./;
-      $start = $list[6];
-      $end = $list[7];
-      if( defined( $clone_offset_hash{$clone} )) {
-
-	$known_clone++;
-	check_line( $clone, $start, $end, $_ );
-      } else {
-	$unknown_clone++;
-      }
-    }
-  }
-  close FH;
-}
-
-sub check_line {
-  my ( $clone, $start, $end, $line ) = @_;
-  my $clonehashref = $clone_offset_hash{$clone};
-  my ( $offset, $length );
-
-  for my $contig ( keys %{$clonehashref} ) {
-    ( $offset, $length ) = @{$clonehashref->{$contig}};
-    # match check
-    if( $start >= $offset && ($end <= ( $offset+$length-1))) {
-      if( defined $contigUsage{$contig} ) {
-	push( @{$contigUsage{$contig}}, $line );
-	$fragmented{$clone}->{$contig} = 1;
-	$double_used_contigs++;
-      } else {
-	push( @{$contigUsage{$contig}}, $line );
-      }
-    }
-    # partly match == mismatch
-    if((( $start < $offset ) && ( $end >= $offset )) ||
-       (( $start <= ($offset+$length-1)) && ( $end > ($offset+$length-1)))) {
-      push( @{$mismatched{$clone}}, $line );
-      $mismatched++;
-      return;
-    }
-  }
-}
-
-sub clone_hash_string {
-  my $clonename = shift;
-  my $hashref = $clone_offset_hash{$clonename};
-  my $result;
-  my @keylist_sorted;
-
-  $result .= "EnsEMBL Freeze Clone $clonename\n";
-  @keylist_sorted = sort { $hashref->{$a}[0] <=> $hashref->{$b}[0] } ( keys %{$hashref} );
-  for my $contig ( @keylist_sorted ) {
-    $result .= "$contig ";
-    my ( $offset, $length );
-    ( $offset, $length ) = @{$hashref->{$contig}};
-    $result .= "$offset ".($offset+$length-1)."\n";
-  }
-
-  return $result;
-}
-
-
 
 find( \&append_agp, $agp_dir );
 print STDERR ( "Reading ", $#filelist+1, " files.\n" );
@@ -113,7 +36,6 @@ for $filename (@filelist) {
   read_agp( $filename );
   $count++;
   if( $count % 100 == 0 ) {
-#    last;
     print STDERR ( "$count read.\n" );
   }
 }
@@ -161,5 +83,82 @@ $mismatched lines were mismatches.
 $unknown_clone lines had unknown clones.
 );
 
-exit;
 
+sub append_agp {
+  /\.agp$/ &&
+    push( @filelist, $File::Find::name );
+}
+
+
+sub read_agp {
+  $filename = shift;
+  local *FH;
+  open( FH, $filename ) or die( "Cant open file $filename." );
+  
+  while( <FH> ) {
+    /^#/ && next;
+    @list = split( /\t/, $_ );
+    if( $list[4] =~ /[^N]/ ) {
+      $readLines++;
+      ( $clone ) = $list[5] =~ /^([^\.]+\.\d+)$/;
+      $start = $list[6];
+      $end = $list[7];
+      if( defined( $clone_offset_hash{$clone} )) {
+
+	$known_clone++;
+	check_line( $clone, $start, $end, $_ );
+      } else {
+	$unknown_clone++;
+	print "Unknown $clone\n";
+      }
+    }
+  }
+  close FH;
+}
+
+
+sub clone_hash_string {
+  my $clonename = shift;
+  my $hashref = $clone_offset_hash{$clonename};
+  my $result;
+  my @keylist_sorted;
+
+  $result .= "EnsEMBL Freeze Clone $clonename\n";
+  @keylist_sorted = sort { $hashref->{$a}[0] <=> $hashref->{$b}[0] } ( keys %{$hashref} );
+  for my $contig ( @keylist_sorted ) {
+    $result .= "$contig ";
+    my ( $offset, $length );
+    ( $offset, $length ) = @{$hashref->{$contig}};
+    $result .= "$offset ".($offset+$length-1)."\n";
+  }
+
+  return $result;
+}
+
+
+sub check_line {
+  my ( $clone, $start, $end, $line ) = @_;
+  my $clonehashref = $clone_offset_hash{$clone};
+  my ( $offset, $length );
+
+  for my $contig ( keys %{$clonehashref} ) {
+    ( $offset, $length ) = @{$clonehashref->{$contig}};
+    # match check
+    if( $start >= $offset && ($end <= ( $offset+$length-1))) {
+      if( defined $contigUsage{$contig} ) {
+	push( @{$contigUsage{$contig}}, $line );
+	$fragmented{$clone}->{$contig} = 1;
+	$double_used_contigs++;
+      } else {
+	push( @{$contigUsage{$contig}}, $line );
+      }
+    }
+    # partly match == mismatch
+    if((( $start < $offset ) && ( $end >= $offset )) ||
+       (( $start <= ($offset+$length-1)) && ( $end > ($offset+$length-1)))) {
+      push( @{$mismatched{$clone}}, $line );
+      $mismatched++;
+      return;
+    }
+  }
+}