Bio::SeqIO qual
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Bio::SeqIO::qual - .qual file input/output stream
Package variables
Privates (from "my" definitions)
$dumper = new Dumpvalue()
Included modules
Do not use this module directly. Use it via the Bio::SeqIO class
(see Bio::SeqIO for details).
  my $in_qual = Bio::SeqIO->new(-file    => $qualfile,
-format => 'qual',
-width => $width,
-verbose => $verbose);
This object can transform .qual (similar to fasta) objects to and from
Bio::Seq::Quality objects. See Bio::Seq::Quality for details.
Like the fasta module, it can take an argument '-width' to change the
number of values per line (defaults to 50).
No description
Methods description
next_seq()code    nextTop
 Title   : next_seq()
Usage : $scf = $stream->next_seq()
Function: returns the next scf sequence in the stream
Returns : Bio::Seq::PrimaryQual object
Notes : Get the next quality sequence from the stream.
 Title   : _next_qual
Usage : $seq = $stream->_next_qual() (but do not do
that. Use $stream->next_seq() instead)
Function: returns the next quality in the stream
Returns : Bio::Seq::PrimaryQual object
Args : NONE
Notes : An internal method. Gets the next quality in
the stream.
 Title   : next_primary_qual()
Usage : $seq = $stream->next_primary_qual()
Function: returns the next sequence in the stream
Returns : Bio::PrimaryQual object
Args : NONE
 Title   : width
Usage : $obj->width($newval)
Function: Get/Set the number of values per line for FASTA-like output
Returns : value of width
Args : newvalue (optional)
 Title   : write_seq
Usage : $obj->write_seq( -source => $source,
-header => "some information"
-oneline => 0);
Function: Write out a list of quality values to a fasta-style file.
Returns : Nothing.
Args : Requires a reference to a Bio::Seq::Quality object or a
PrimaryQual object as the -source. Option 1: information
for the header. Option 2: whether the quality score should
be on a single line or not
Notes : If no -header is provided, $obj->id() will be used where
$obj is a reference to either a Quality object or a
PrimaryQual object. If $source->id() fails, "unknown" will
be the header. If the Quality object has $source->length()
of "DIFFERENT" (read the pod, luke), write_seq will use the
length of the PrimaryQual object within the Quality object.
Methods code
sub _initialize {
    my($self,@args) = @_;
    my ($width) = $self->_rearrange([qw(WIDTH)], @args);
    $width && $self->width($width);
    if( ! defined $self->sequence_factory ) {
                                (-verbose => $self->verbose(),
                                 -type => 'Bio::Seq::PrimaryQual'));
sub next_seq {
    my ($self,@args) = @_;
    my ($qual,$seq);
    my $alphabet;
    local $/ = "\n>";

    return unless my $entry = $self->_readline;

    if ($entry eq '>') {	# very first one
return unless $entry = $self->_readline; } # original: my ($top,$sequence) = $entry =~ /^(.+?)\n([^>]*)/s
my ($top,$sequence) = $entry =~ /^(.+?)\n([^>]*)/s or $self->throw("Can't parse entry [$entry]"); my ($id,$fulldesc) = $top =~ /^\s*(\S+)\s*(.*)/ or $self->throw("Can't parse fasta header"); $id =~ s/^>//; # create the seq object
$sequence =~ s/\n+/ /g; return $self->sequence_factory->create (-qual => $sequence, -id => $id, -primary_id => $id, -display_id => $id, -desc => $fulldesc );
sub _next_qual {
    my $qual = next_primary_qual( $_[0], 1 );
    return $qual;
sub next_primary_qual {
    # print("CSM next_primary_qual!\n");
my( $self, $as_next_qual ) = @_; my ($qual,$seq); local $/ = "\n>"; return unless my $entry = $self->_readline; if ($entry eq '>') { # very first one
return unless $entry = $self->_readline; } my ($top,$sequence) = $entry =~ /^(.+?)\n([^>]*)/s or $self->throw("Can't parse entry [$entry]"); my ($id,$fulldesc) = $top =~ /^\s*(\S+)\s*(.*)/ or $self->throw("Can't parse fasta header"); $id =~ s/^>//; # create the seq object
$sequence =~ s/\n+/ /g; if ($as_next_qual) { $qual = Bio::Seq::PrimaryQual->new(-qual => $sequence, -id => $id, -primary_id => $id, -display_id => $id, -desc => $fulldesc ); } return $qual;
sub width {
   my ($self,$value) = @_;
   if( defined $value) {
      $self->{'width'} = $value;
    return $self->{'width'} || $WIDTH;
sub write_seq {
    my ($self,@args) = @_;
    my $width = $self->width;
    my ($source, $head, $oneline) = $self->_rearrange([qw(SOURCE HEADER ONELINE)], @args);
    if (!$source || ( !$source->isa('Bio::Seq::Quality') &&
                      !$source->isa('Bio::Seq::PrimaryQual')   )) {
        $self->throw("You must pass a Bio::Seq::Quality or a Bio::Seq::PrimaryQual".
                     " object to write_seq() as a parameter named\" source\"");
    my $header = ($source->can("header") && $source->header) ?
        $source->header :
            ($source->can("id") && $source->id) ?
                $source->id :
    my @quals = $source->qual();
    # ::dumpValue(\@quals);
my $desc = $source->desc if $source->can('desc'); $desc ||= ''; $self->_print (">$header $desc\n"); my (@slice,$max,$length); $length = $source->length(); if ( not(defined($oneline)) || $oneline == 0) { # $width quality values per line
for (my $count = 1; $count<=$length; $count+= $width) { if ($count+$width > $length) { $max = $length; } else { $max = $count+$width-1; } my @slice = @{$source->subqual($count,$max)}; $self->_print (join(' ',@slice), "\n"); } } else { # quality values on a single line
my @slice = @{$source->qual}; $self->_print (join(' ',@slice), "\n"); } $self->flush if $self->_flush_on_write && defined $self->_fh; return 1; } 1; __END__
General documentation
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address it. Please include a thorough description of the problem
with code and data examples if at all possible.
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AUTHOR Chad MatsallaTop
Chad Matsalla
Jason Stajich,
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _