Bio::SeqIO qual
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Summary
Bio::SeqIO::qual - .qual file input/output stream
Package variables
Privates (from "my" definitions)
$dumper = new Dumpvalue()
Included modules
Bio::Seq::SeqFactory
Dumpvalue
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
_initialize
No description
Code
next_seqDescriptionCode
_next_qualDescriptionCode
next_primary_qualDescriptionCode
widthDescriptionCode
write_seqDescriptionCode
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.
_next_qualcodeprevnextTop
 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.
next_primary_qual()codeprevnextTop
 Title   : next_primary_qual()
Usage : $seq = $stream->next_primary_qual()
Function: returns the next sequence in the stream
Returns : Bio::PrimaryQual object
Args : NONE
widthcodeprevnextTop
 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)
write_seqcodeprevnextTop
 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 $source->length()
of "DIFFERENT" (read the pod, luke), write_seq will use the
length of the PrimaryQual object within the Quality object.
Methods code
_initializedescriptionprevnextTop
sub _initialize {
    my($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 => $self->verbose(),
                                 -type => 'Bio::Seq::PrimaryQual'));
    }
}
next_seqdescriptionprevnextTop
sub next_seq {
    my ($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 );
}
_next_qualdescriptionprevnextTop
sub _next_qual {
    my $qual = next_primary_qual( $_[0], 1 );
    return $qual;
}
next_primary_qualdescriptionprevnextTop
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 $qual;
}
widthdescriptionprevnextTop
sub width {
   my ($self,$value) = @_;
   if( defined $value) {
      $self->{'width'} = $value;
    }
    return $self->{'width'} || $WIDTH;
}
write_seqdescriptionprevnextTop
sub write_seq {
    my ($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
FEEDBACKTop
Mailing ListsTop
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
Support Top
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.
Reporting BugsTop
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/
AUTHOR Chad MatsallaTop
Chad Matsalla bioinformatics@dieselwurks.com
CONTRIBUTORSTop
Jason Stajich, jason@bioperl.org
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _