Toolbar

Summary

Bio::SeqIO::qual - .qual file input/output stream

Package variables

Included modules

Inherit

Bio::SeqIO

Synopsis

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);

Description

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).

Methods

Methods description

 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) = @_;
    $self->SUPER::_initialize(@args);
    my ($width) = $self->_rearrange([qw(WIDTH)], @args);
    $width && $self->width($width);
    if( ! defined $self->sequence_factory ) {
        $self->sequence_factory(Bio::Seq::SeqFactory->new
                                (-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 :
                    "unknown";
    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

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.

Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via the web:

  https://redmine.open-bio.org/projects/bioperl/

Chad Matsalla bioinformatics@dieselwurks.com

Jason Stajich, jason@bioperl.org

The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _