added BED entry output to check_bed

[biopieces.git] / code_perl / Maasha / UCSC / BED.pm

diff --git a/code_perl/Maasha/UCSC/BED.pm b/code_perl/Maasha/UCSC/BED.pm
index 6bfa590b364d486f8202ddc454793b24d5fbc21d..3d873e660ec6d85b92a48b341e7c5fe940a4cd9c 100644 (file)
--- a/code_perl/Maasha/UCSC/BED.pm
+++ b/code_perl/Maasha/UCSC/BED.pm
@@ -188,121 +188,122 @@ sub bed_entry_check
 
     # Returns nothing.
 
-    my ( $cols, @block_sizes, @block_starts );
+    my ( $entry, $cols, @block_sizes, @block_starts );
 
-    $cols = scalar @{ $bed };
+    $entry = join "\t", @{ $bed };
+    $cols  = scalar @{ $bed };
 
     if ( $cols < 3 ) {
-        Maasha::Common::error( qq(Bad BED entry - must contain at least 3 columns - not $cols) );
+        Maasha::Common::error( qq(Bad BED entry "$entry" - must contain at least 3 columns - not $cols) );
     }
 
     if ( $cols > 12 ) {
-        Maasha::Common::error( qq(Bad BED entry - must contains no more than 12 columns - not $cols) );
+        Maasha::Common::error( qq(Bad BED entry "$entry" - must contains no more than 12 columns - not $cols) );
     }
 
     if ( $bed->[ chrom ] =~ /\s/ ) {
-        Maasha::Common::error( qq(Bad BED entry - no white space allowed in chrom field: "$bed->[ chrom ]") );
+        Maasha::Common::error( qq(Bad BED entry "$entry" - no white space allowed in chrom field: "$bed->[ chrom ]") );
     }
 
     if ( $bed->[ chromStart ] =~ /\D/ ) {
-        Maasha::Common::error( qq(Bad BED entry - chromStart must be a whole number - not "$bed->[ chromStart ]") );
+        Maasha::Common::error( qq(Bad BED entry "$entry" - chromStart must be a whole number - not "$bed->[ chromStart ]") );
     }
 
     if ( $bed->[ chromEnd ] =~ /\D/ ) {
-        Maasha::Common::error( qq(Bad BED entry - chromEnd must be a whole number - not "$bed->[ chromEnd ]") );
+        Maasha::Common::error( qq(Bad BED entry "$entry" - chromEnd must be a whole number - not "$bed->[ chromEnd ]") );
     }
 
     if ( $bed->[ chromEnd ] < $bed->[ chromStart ] ) {
-        Maasha::Common::error( qq(Bad BED entry - chromEnd must be greater than chromStart - not "$bed->[ chromStart ] > $bed->[ chromEnd ]") );
+        Maasha::Common::error( qq(Bad BED entry "$entry" - chromEnd must be greater than chromStart - not "$bed->[ chromStart ] > $bed->[ chromEnd ]") );
     }
 
     return if $cols == 3;
 
     if ( $bed->[ name ] =~ /\s/ ) {
-        Maasha::Common::error( qq(Bad BED entry - no white space allowed in name field: "$bed->[ name ]") );
+        Maasha::Common::error( qq(Bad BED entry "$entry" - no white space allowed in name field: "$bed->[ name ]") );
     }
 
     return if $cols == 4;
 
     if ( $bed->[ score ] =~ /\D/ ) {
-        Maasha::Common::error( qq(Bad BED entry - score must be a whole number - not "$bed->[ score ]") );
+        Maasha::Common::error( qq(Bad BED entry "$entry" - score must be a whole number - not "$bed->[ score ]") );
     }
 
     # if ( $bed->[ score ] < 0 or $bed->[ score ] > 1000 ) { # disabled - too restrictive !
     if ( $bed->[ score ] < 0 ) {
-        Maasha::Common::error( qq(Bad BED entry - score must be between 0 and 1000 - not "$bed->[ score ]") );
+        Maasha::Common::error( qq(Bad BED entry "$entry" - score must be between 0 and 1000 - not "$bed->[ score ]") );
     }
 
     return if $cols == 5;
 
     if ( $bed->[ strand ] ne '+' and $bed->[ strand ] ne '-' ) {
-        Maasha::Common::error( qq(Bad BED entry - strand must be + or - not "$bed->[ strand ]") );
+        Maasha::Common::error( qq(Bad BED entry "$entry" - strand must be + or - not "$bed->[ strand ]") );
     }
 
     return if $cols == 6;
 
     if ( $bed->[ thickStart ] =~ /\D/ ) {
-        Maasha::Common::error( qq(Bad BED entry - thickStart must be a whole number - not "$bed->[ thickStart ]") );
+        Maasha::Common::error( qq(Bad BED entry "$entry" - thickStart must be a whole number - not "$bed->[ thickStart ]") );
     }
 
     if ( $bed->[ thickEnd ] =~ /\D/ ) {
-        Maasha::Common::error( qq(Bad BED entry - thickEnd must be a whole number - not "$bed->[ thickEnd ]") );
+        Maasha::Common::error( qq(Bad BED entry "$entry" - thickEnd must be a whole number - not "$bed->[ thickEnd ]") );
     }
 
     if ( $bed->[ thickEnd ] < $bed->[ thickStart ] ) {
-        Maasha::Common::error( qq(Bad BED entry - thickEnd must be greater than thickStart - not "$bed->[ thickStart ] > $bed->[ thickEnd ]") );
+        Maasha::Common::error( qq(Bad BED entry "$entry" - thickEnd must be greater than thickStart - not "$bed->[ thickStart ] > $bed->[ thickEnd ]") );
     }
 
     if ( $bed->[ thickStart ] < $bed->[ chromStart ] ) {
-        Maasha::Common::error( qq(Bad BED entry - thickStart must be greater than chromStart - not "$bed->[ thickStart ] < $bed->[ chromStart ]") );
+        Maasha::Common::error( qq(Bad BED entry "$entry" - thickStart must be greater than chromStart - not "$bed->[ thickStart ] < $bed->[ chromStart ]") );
     }
 
     if ( $bed->[ thickStart ] > $bed->[ chromEnd ] ) {
-        Maasha::Common::error( qq(Bad BED entry - thickStart must be less than chromEnd - not "$bed->[ thickStart ] > $bed->[ chromEnd ]") );
+        Maasha::Common::error( qq(Bad BED entry "$entry" - thickStart must be less than chromEnd - not "$bed->[ thickStart ] > $bed->[ chromEnd ]") );
     }
 
     if ( $bed->[ thickEnd ] < $bed->[ chromStart ] ) {
-        Maasha::Common::error( qq(Bad BED entry - thickEnd must be greater than chromStart - not "$bed->[ thickEnd ] < $bed->[ chromStart ]") );
+        Maasha::Common::error( qq(Bad BED entry "$entry" - thickEnd must be greater than chromStart - not "$bed->[ thickEnd ] < $bed->[ chromStart ]") );
     }
 
     if ( $bed->[ thickEnd ] > $bed->[ chromEnd ] ) {
-        Maasha::Common::error( qq(Bad BED entry - thickEnd must be less than chromEnd - not "$bed->[ thickEnd ] > $bed->[ chromEnd ]") );
+        Maasha::Common::error( qq(Bad BED entry "$entry" - thickEnd must be less than chromEnd - not "$bed->[ thickEnd ] > $bed->[ chromEnd ]") );
     }
 
     return if $cols == 8;
 
     if ( $bed->[ itemRgb ] !~ /^(0|\d{1,3},\d{1,3},\d{1,3},?)$/ ) {
-        Maasha::Common::error( qq(Bad BED entry - itemRgb must be 0 or in the form of 255,0,0 - not "$bed->[ itemRgb ]") );
+        Maasha::Common::error( qq(Bad BED entry "$entry" - itemRgb must be 0 or in the form of 255,0,0 - not "$bed->[ itemRgb ]") );
     }
 
     return if $cols == 9;
 
     if ( $bed->[ blockCount ] =~ /\D/ ) {
-        Maasha::Common::error( qq(Bad BED entry - blockCount must be a whole number - not "$bed->[ blockCount ]") );
+        Maasha::Common::error( qq(Bad BED entry "$entry" - blockCount must be a whole number - not "$bed->[ blockCount ]") );
     }
 
     @block_sizes = split ",", $bed->[ blockSizes ];
 
     if ( grep /\D/, @block_sizes ) {
-        Maasha::Common::error( qq(Bad BED entry - blockSizes must be whole numbers - not "$bed->[ blockSizes ]") );
+        Maasha::Common::error( qq(Bad BED entry "$entry" - blockSizes must be whole numbers - not "$bed->[ blockSizes ]") );
     }
 
     if ( $bed->[ blockCount ] != scalar @block_sizes ) {
-        Maasha::Common::error( qq(Bad BED entry - blockSizes "$bed->[ blockSizes ]" must match blockCount "$bed->[ blockCount ]") );
+        Maasha::Common::error( qq(Bad BED entry "$entry" - blockSizes "$bed->[ blockSizes ]" must match blockCount "$bed->[ blockCount ]") );
     }
 
     @block_starts = split ",", $bed->[ blockStarts ];
 
     if ( grep /\D/, @block_starts ) {
-        Maasha::Common::error( qq(Bad BED entry - blockStarts must be whole numbers - not "$bed->[ blockStarts ]") );
+        Maasha::Common::error( qq(Bad BED entry "$entry" - blockStarts must be whole numbers - not "$bed->[ blockStarts ]") );
     }
 
     if ( $bed->[ blockCount ] != scalar @block_starts ) {
-        Maasha::Common::error( qq(Bad BED entry - blockStarts "$bed->[ blockStarts ]" must match blockCount "$bed->[ blockCount ]") );
+        Maasha::Common::error( qq(Bad BED entry "$entry" - blockStarts "$bed->[ blockStarts ]" must match blockCount "$bed->[ blockCount ]") );
     }
 
     if ( $bed->[ chromStart ] + $block_starts[ -1 ] + $block_sizes[ -1 ] != $bed->[ chromEnd ] ) {
-        Maasha::Common::error( qq(Bad BED entry - chromStart + blockStarts[last] + blockSizes[last] must equal chromEnd: ) .
+        Maasha::Common::error( qq(Bad BED entry "$entry" - chromStart + blockStarts[last] + blockSizes[last] must equal chromEnd: ) .
                                qq($bed->[ chromStart ] + $block_starts[ -1 ] + $block_sizes[ -1 ] != $bed->[ chromEnd ]) );
     }
 }