#
# Copyright (c) 1997-9 bioperl, Chad Matsalla. All Rights Reserved.
# This module is free software; you can redistribute it and/or
# modify it under the same terms as Perl itself.
#
# Copyright Chad Matsalla
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::SeqIO::qual - .qual file input/output stream
=head1 SYNOPSIS
Do not use this module directly. Use it via the Bio::SeqIO class
(see L<Bio::SeqIO> for details).
my $in_qual = Bio::SeqIO->new(-file => $qualfile,
-format => 'qual',
-width => $width,
-verbose => $verbose);
=head1 DESCRIPTION
This object can transform .qual (similar to fasta) objects to and from
Bio::Seq::Quality objects. See L<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).
=head1 FEEDBACK
=head2 Mailing Lists
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
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<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.
=head2 Reporting Bugs
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://github.com/bioperl/bioperl-live/issues
=head1 AUTHOR Chad Matsalla
Chad Matsalla
bioinformatics@dieselwurks.com
=head1 CONTRIBUTORS
Jason Stajich, jason@bioperl.org
=head1 APPENDIX
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::SeqIO::qual;
use strict;
use Bio::Seq::SeqFactory;
use Dumpvalue;
my $dumper = Dumpvalue->new();
use base qw(Bio::SeqIO);
our $WIDTH = 25;
sub _initialize {
my($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'));
}
}
=head2 next_seq()
Title : next_seq()
Usage : $scf = $stream->next_seq()
Function: returns the next scf sequence in the stream
Returns : Bio::Seq::PrimaryQual object
Notes : Get the next quality sequence from the stream.
=cut
sub next_seq {
my ($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
);
}
=head2 _next_qual
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.
=cut
sub _next_qual {
my $qual = next_primary_qual( $_[0], 1 );
return $qual;
}
=head2 next_primary_qual()
Title : next_primary_qual()
Usage : $seq = $stream->next_primary_qual()
Function: returns the next sequence in the stream
Returns : Bio::PrimaryQual object
Args : NONE
=cut
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;
}
=head2 width
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)
=cut
sub width{
my ($self,$value) = @_;
if( defined $value) {
$self->{'width'} = $value;
}
return $self->{'width'} || $WIDTH;
}
=head2 write_seq
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 $source->length()
of "DIFFERENT" (read the pod, luke), write_seq will use the
length of the PrimaryQual object within the Quality object.
=cut
sub write_seq {
my ($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__