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).

Description

This object can transform .qual (similar to fasta) objects to and from
Bio::Seq::SeqWithQuality objects. See Bio::Seq::SeqWithQuality for
details.

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   : write_seq(-source => $source, -header => "some information")
 Usage   : $obj->write_seq(	-source => $source,
				-header => "some information");
 Function: Write out an list of quality values to a fasta-style file.
 Returns : Nothing.
 Args    : Requires: a reference to a SeqWithQuality object or a
	PrimaryQual object as the -source. Optional: information
	for the header.
 Notes   : If no -header is provided, $obj->id() will be used where
	$obj is a reference to either a SeqWithQuality object or a
	PrimaryQual object. If $source->id() fails, ">unknown" will be
	the header. If the SeqWithQuality object has $source->length() of
	"DIFFERENT" (read the pod, luke), write_seq will use the length
	of the PrimaryQual object within the SeqWithQuality object.

Methods code

sub _initialize {

  my($self,@args) = @_;
  $self->SUPER::_initialize(@args);    
  if( ! defined $self->sequence_factory ) {
      $self->sequence_factory(new Bio::Seq::SeqFactory
			      (-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 write_seq {

    my ($self,@args) = @_;
    my ($source)  = $self->_rearrange([qw(SOURCE)], @args);

    if (!$source || ( !$source->isa('Bio::Seq::SeqWithQuality') && 
		      !$source->isa('Bio::Seq::PrimaryQual')   )) {
	$self->throw("You must pass a Bio::Seq::SeqWithQuality or a Bio::Seq::PrimaryQual object to write_seq as a parameter named\" source\"");
    }
    my $header = $source->id();
    if (!$header) { $header = "unknown"; }
    my @quals = $source->qual();
    # ::dumpValue(\@quals);
    $self->_print (">$header\n ");
    my (@slice,$max,$length);
    $length = $source->length();
    if ($length eq "DIFFERENT") {
	$self->warn("You passed a SeqWithQuality object that contains a sequence and quality of differing lengths. Using the length of the PrimaryQual component of the SeqWithQuality object.");
	$length = $source->qual_obj()->length();
    }
    # print("Printing $header to a file.\n");
    for (my $count = 1; $count<=$length; $count+= 50) {
	if ($count+50 > $length) { $max = $length; }
	else { $max = $count+49; }
	my @slice = @{$source->subqual($count,$max)};
	$self->_print (join(' ',@slice), "\n");
    }

    $self->flush if $self->_flush_on_write && defined $self->_fh;
    return 1;

}

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

  bioperl-bugs@bio.perl.org
  http://bugzilla.bioperl.org/

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 _