disabled quality score conversion in FASTQ and Solexa

[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 f2a11e8c8ba95ce85745f6dc2a98b21f004dffa8..6bfa590b364d486f8202ddc454793b24d5fbc21d 100644 (file)
--- a/code_perl/Maasha/UCSC/BED.pm
+++ b/code_perl/Maasha/UCSC/BED.pm
@@ -30,6 +30,7 @@ package Maasha::UCSC::BED;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 
 use Data::Dumper;
@@ -74,9 +75,6 @@ use constant {
 };
 
 
-my $CHECK_ALL = 1;   # Global flag indicating that BED input and output is checked thoroughly.
-
-
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> BED format <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
@@ -123,7 +121,8 @@ sub bed_entry_get
     # Reads a BED entry given a filehandle.
 
     my ( $fh,     # file handle
-         $cols,   # columns to read - OPTIONAL (3,4,5,6,8,9 or 12)
+         $cols,   # columns to read               - OPTIONAL (3,4,5,6,8,9 or 12)
+         $check,  # check integrity of BED values - OPTIONAL
        ) = @_;
 
     # Returns a list.
@@ -132,10 +131,10 @@ sub bed_entry_get
 
     $line = <$fh>;
 
-    $line =~ tr/\n\r//d;    # some people have carriage returns in their BED files -> Grrrr
-
     return if not defined $line;
 
+    $line =~ tr/\n\r//d;    # some people have carriage returns in their BED files -> Grrrr
+
     if ( not defined $cols ) {
         $cols = 1 + $line =~ tr/\t//;
     }
@@ -144,7 +143,7 @@ sub bed_entry_get
 
     pop @entry if scalar @entry > $cols;
 
-    bed_entry_check( \@entry ) if $CHECK_ALL;
+    bed_entry_check( \@entry ) if $check;
 
     return wantarray ? @entry : \@entry;
 }
@@ -159,6 +158,7 @@ sub bed_entry_put
     my ( $entry,   # list
          $fh,      # file handle                   - OPTIONAL
          $cols,    # number of columns in BED file - OPTIONAL (3,4,5,6,8,9 or 12)
+         $check,   # check integrity of BED values - OPTIONAL
        ) = @_;
 
     # Returns nothing.
@@ -167,7 +167,7 @@ sub bed_entry_put
         @{ $entry } = @{ $entry }[ 0 .. $cols - 1 ];
     }
 
-    bed_entry_check( $entry ) if $CHECK_ALL;
+    bed_entry_check( $entry ) if $check;
 
     $fh = \*STDOUT if not defined $fh;
 
@@ -216,29 +216,30 @@ sub bed_entry_check
         Maasha::Common::error( qq(Bad BED entry - chromEnd must be greater than chromStart - not "$bed->[ chromStart ] > $bed->[ chromEnd ]") );
     }
 
-    return if @{ $bed } == 3;
+    return if $cols == 3;
 
     if ( $bed->[ name ] =~ /\s/ ) {
         Maasha::Common::error( qq(Bad BED entry - no white space allowed in name field: "$bed->[ name ]") );
     }
 
-    return if @{ $bed } == 4;
+    return if $cols == 4;
 
     if ( $bed->[ score ] =~ /\D/ ) {
         Maasha::Common::error( qq(Bad BED entry - score must be a whole number - not "$bed->[ score ]") );
     }
 
-    if ( $bed->[ score ] < 0 or $bed->[ score ] > 1000 ) {
+    # 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 ]") );
     }
 
-    return if @{ $bed } == 5;
+    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 ]") );
     }
 
-    return if @{ $bed } == 6;
+    return if $cols == 6;
 
     if ( $bed->[ thickStart ] =~ /\D/ ) {
         Maasha::Common::error( qq(Bad BED entry - thickStart must be a whole number - not "$bed->[ thickStart ]") );
@@ -268,13 +269,13 @@ sub bed_entry_check
         Maasha::Common::error( qq(Bad BED entry - thickEnd must be less than chromEnd - not "$bed->[ thickEnd ] > $bed->[ chromEnd ]") );
     }
 
-    return if @{ $bed } == 8;
+    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 ]") );
     }
 
-    return if @{ $bed } == 9;
+    return if $cols == 9;
 
     if ( $bed->[ blockCount ] =~ /\D/ ) {
         Maasha::Common::error( qq(Bad BED entry - blockCount must be a whole number - not "$bed->[ blockCount ]") );
@@ -418,7 +419,7 @@ sub bed2biopiece
     $bp_record{ "CHR" }      = $bed_entry->[ chrom ];
     $bp_record{ "CHR_BEG" }  = $bed_entry->[ chromStart ];
     $bp_record{ "CHR_END" }  = $bed_entry->[ chromEnd ] - 1;
-    $bp_record{ "BED_LEN" }  = $bed_entry->[ chromEnd ] - $bed_entry->[ chromEnd ];
+    $bp_record{ "BED_LEN" }  = $bed_entry->[ chromEnd ] - $bed_entry->[ chromStart ];
 
     return wantarray ? %bp_record : \%bp_record if $cols == 3;
 
@@ -471,7 +472,7 @@ sub biopiece2bed
 
     # Returns arrayref.
 
-    my ( @bed_entry );
+    my ( @bed_entry, @begs );
 
     $cols ||= 12;   # max number of columns possible
 
@@ -479,13 +480,21 @@ sub biopiece2bed
                                $bp_record->{ "S_ID" }    ||
                                return undef;
 
-    $bed_entry[ chromStart ] = $bp_record->{ "CHR_BEG" } || 
-                               $bp_record->{ "S_BEG" }   ||
-                               return undef;
+    if ( defined $bp_record->{ "CHR_BEG" } ) {
+        $bed_entry[ chromStart ] = $bp_record->{ "CHR_BEG" };
+    } elsif ( defined $bp_record->{ "S_BEG" } ) {
+        $bed_entry[ chromStart ] = $bp_record->{ "S_BEG" };
+    } else {
+        return undef;
+    }
 
-    $bed_entry[ chromEnd ]   = $bp_record->{ "CHR_END" } || 
-                               $bp_record->{ "S_END" }   ||
-                               return undef;
+    if ( defined $bp_record->{ "CHR_END" } ) {
+        $bed_entry[ chromEnd ] = $bp_record->{ "CHR_END" };
+    } elsif ( defined $bp_record->{ "S_END" }) {
+        $bed_entry[ chromEnd ] = $bp_record->{ "S_END" };
+    } else {
+        return undef;
+    }
 
     $bed_entry[ chromEnd ]++;
 
@@ -515,27 +524,47 @@ sub biopiece2bed
          defined $bp_record->{ "THICK_END" } )
     {
         $bed_entry[ thickStart ] = $bp_record->{ "THICK_BEG" };
-        $bed_entry[ thickEnd ]   = $bp_record->{ "THICK_END" };
+        $bed_entry[ thickEnd ]   = $bp_record->{ "THICK_END" } + 1;
+    }
+    elsif ( defined $bp_record->{ "BLOCK_COUNT" } )
+    {
+        $bed_entry[ thickStart ] = $bed_entry[ chromStart ];
+        $bed_entry[ thickEnd ]   = $bed_entry[ chromEnd ];
     }
 
     return wantarray ? @bed_entry : \@bed_entry if $cols == 8;
 
-    if ( exists $bp_record->{ "COLOR" } ) {
+    if ( defined $bp_record->{ "COLOR" } )
+    {
         $bed_entry[ itemRgb ] = $bp_record->{ "COLOR" };
-    } else {
-        return wantarray ? @bed_entry : \@bed_entry;
+    }
+    elsif ( defined $bp_record->{ "BLOCK_COUNT" } )
+    {
+        $bed_entry[ itemRgb ] = 0;
     }
 
     return wantarray ? @bed_entry : \@bed_entry if $cols == 9;
 
     if ( defined $bp_record->{ "BLOCK_COUNT" } and
+         defined $bp_record->{ "BLOCK_LENS" }  and
+         defined $bp_record->{ "S_BEGS" } )
+    {
+        @begs = split ",", $bp_record->{ "S_BEGS" };
+        map { $_ -= $bed_entry[ chromStart ] } @begs;
+
+        $bed_entry[ blockCount ]  = $bp_record->{ "BLOCK_COUNT" };
+        $bed_entry[ blockSizes ]  = $bp_record->{ "BLOCK_LENS" };
+        $bed_entry[ blockStarts ] = join ",", @begs;
+        $bed_entry[ thickEnd ]    = $bp_record->{ "THICK_END" } + 1;
+    }
+    elsif ( defined $bp_record->{ "BLOCK_COUNT" } and
          defined $bp_record->{ "BLOCK_LENS" }  and
          defined $bp_record->{ "Q_BEGS" } )
     {
         $bed_entry[ blockCount ]  = $bp_record->{ "BLOCK_COUNT" };
         $bed_entry[ blockSizes ]  = $bp_record->{ "BLOCK_LENS" };
         $bed_entry[ blockStarts ] = $bp_record->{ "Q_BEGS" };
-        $bed_entry[ thickEnd ]++;
+        $bed_entry[ thickEnd  ]   = $bp_record->{ "THICK_END" } + 1;
     }
 
     return wantarray ? @bed_entry : \@bed_entry;
@@ -553,6 +582,7 @@ sub tag_contigs_assemble
 
     my ( $bed_file,   # path to BED file
          $chr,        # chromosome
+         $strand,     # strand
          $dir,        # working directory
        ) = @_;
          
@@ -580,6 +610,7 @@ sub tag_contigs_assemble
         $entry->[ chromEnd ]   = $end;
         $entry->[ name ]       = sprintf( "TC%06d", $id );
         $entry->[ score ]      = $score;
+        $entry->[ strand ]     = $strand;
 
         bed_entry_put( $entry, $fh_out );