#
# Copyright (c) 1997-2001 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::phd - phd file input/output stream
=head1 SYNOPSIS
Do not use this module directly. Use it via the L<Bio::SeqIO> class.
=head1 DESCRIPTION
This object can transform .phd files (from Phil Green's phred basecaller)
to and from Bio::Seq::Quality objects. The phd format is described in section 10
at this url: http://www.phrap.org/phredphrap/phred.html
=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
Jean-Marc Frigerio, Frigerio@pierroton.inra.fr
=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::phd;
use strict;
use Bio::Seq::SeqFactory;
use Bio::Seq::RichSeq;
use Bio::Annotation::Collection;
use Bio::Annotation::Comment;
use Dumpvalue;
my $dumper = Dumpvalue->new();
use base qw(Bio::SeqIO);
sub _initialize {
my($self,@args) = @_;
$self->SUPER::_initialize(@args);
if( ! defined $self->sequence_factory ) {
$self->sequence_factory(Bio::Seq::SeqFactory->new
(-verbose => $self->verbose(),
-type => 'Bio::Seq::Quality'));
}
}
=head2 next_seq
Title : next_seq()
Usage : $swq = $stream->next_seq()
Function: returns the next phred sequence in the stream
Returns : Bio::Seq::Quality object
Args : NONE
=cut
sub next_seq {
my ($self,@args) = @_;
my $seq;
while (my $entry = $self->_readline) {
chomp $entry;
if ($entry =~ /^BEGIN_SEQUENCE\s+(\S+)/) {
if (defined $seq) {
# done with current sequence
$self->_pushback($entry);
last;
} else {
# start new sequence
my $id = $1;
$seq = $self->sequence_factory->create(
-id => $id,
-primary_id => $id,
-display_id => $id,
);
}
} elsif ($entry =~ /^BEGIN_COMMENT/) {
my $collection = Bio::Annotation::Collection->new;
while ($entry = $self->_readline) {
chomp $entry;
if ($entry =~ /^(\w+):\s+(.+)$/) {
my ($name, $content) = ($1, $2);
my $comment = Bio::Annotation::Comment->new(
-text => $content,
-tagname => $name
);
$collection->add_Annotation('header',$comment);
} elsif ($entry =~ /^END_COMMENT/) {
$seq->Bio::Seq::RichSeq::annotation($collection);
last;
}
}
} elsif ($entry =~ /^BEGIN_DNA/) {
my $dna = '';
my @qualities = ();
my @trace_indices = ();
while ($entry = $self->_readline) {
chomp $entry;
if ( $entry =~ /(\S+)\s+(\S+)\s+(\S+)/ ) {
# add nucleotide and quality scores to sequence
$dna .= $1;
push @qualities,$2;
push(@trace_indices,$3) if defined $3; # required for phd file
} elsif ($entry =~ /^END_DNA/) {
# end of sequence, save it
$seq->seq($dna);
$seq->qual(\@qualities);
$seq->trace(\@trace_indices);
last;
}
}
} elsif ($entry =~ /^END_SEQUENCE/) {
# the sequence may be over, but some other info can come after
next;
} elsif ($entry =~ /^WR{/) {
# Whole-Read items
# Programs like Consed or Autofinish add it to phd file. See doc:
# http://www.phrap.org/consed/distributions/README.16.0.txt
#my ($type, $nane, $date, $time) = split(' ',$self->_readline);
#my $extra_info = '';
#while ($entry = $self->_readline) {
# chomp $entry;
# last if ($entry =~ /\}/);
# $extra_info .= $entry;
#}
### fea: save WR somewhere? but where?
}
}
return $seq;
}
=head2 write_header
Title : write_header()
Usage : $seqio->write_header()
Function: Write out the header (BEGIN_COMMENTS .. END_COMMENT) part of a phd file
Returns : nothing
Args : a Bio::Seq::Quality object
Notes : These are the comments that reside in the header of a phd file
at the present time. If not provided by the Bio::Seq::Quality object,
the following default values will be used:
CHROMAT_FILE : $swq->id()
ABI_THUMBPRINT : 0
PHRED_VERSION : 0.980904.e
CALL_METHOD : phred
QUALITY_LEVELS : 99
TIME : <current time>
TRACE_ARRAY_MIN_INDEX : 0
TRACE_ARRAY_MAX_INDEX : unknown
CHEM : unknown
DYE : unknown
=cut
sub write_header {
my ($self, $swq) = @_;
$self->_print("\nBEGIN_COMMENT\n\n");
#defaults
my $time = localtime();
for ([CHROMAT_FILE =>$swq->attribute('CHROMAT_FILE')],
[ABI_THUMBPRINT => 0],
[PHRED_VERSION => '0.980904.e'],
[CALL_METHOD => 'phred'],
[QUALITY_LEVELS => '99'],
[TIME => $time],
[TRACE_ARRAY_MIN_INDEX => 0],
[TRACE_ARRAY_MAX_INDEX => 'unknown'],
[CHEM => 'unknown'],
[DYE => 'unknown'])
{
$swq->attribute($_->[0],$_->[1]) unless $swq->attribute($_->[0]);
}
my @annot = $swq->annotation->get_Annotations('header');
for (@annot) {
$self->_print($_->tagname,": ",$_->text,"\n");
}
$self->_print("\nEND_COMMENT\n\n");
$self->flush if $self->_flush_on_write && defined $self->_fh;
return 1;
}
=head2 write_seq
Title : write_seq()
Usage : $seqio->write_seq($swq);
Function: Write out a phd file.
Returns : Nothing.
Args : a Bio::Seq::Quality object
=cut
sub write_seq {
my ($self,$swq) = @_;
$self->throw("You must pass a Bio::Seq::Quality object to write_seq")
unless (ref($swq) eq "Bio::Seq::Quality");
$self->throw("Can't create the phd because the sequence and the quality in the Quality object are of different lengths.")
unless $swq->length() ne 'DIFFERENT';
$self->_print("BEGIN_SEQUENCE ".$swq->id()."\n");
$self->write_header($swq);
$self->_print("BEGIN_DNA\n");
for my $curr(1 .. $swq->length()) {
$self->_print (sprintf("%s %s %s\n",
uc($swq->baseat($curr)),
$swq->qualat($curr),
$swq->trace_index_at($curr)));
}
$self->_print ("END_DNA\n\nEND_SEQUENCE\n");
$self->flush if $self->_flush_on_write && defined $self->_fh;
return 1;
}
=head2 attribute
Title : attribute()
Usage : swq->attribute(name[,value]);
Function: Get/Set the name attribute.
Returns : a string if 1 param, nothing else.
Args : a name or a pair name, value
=cut
sub Bio::Seq::Quality::attribute {
my ($self, $name, $value) = @_;
my $collection = $self->annotation;
my @annot = $collection->get_Annotations('header');
my %attribute;
my $annot;
for (@annot) {
$attribute{$_->tagname} = $_->display_text;
$annot = $_ if $_->tagname eq $name;
}
unless (defined $attribute{$name}) { #new comment
my $comment =
Bio::Annotation::Comment->new(-text => $value || 'unknown');
$comment->tagname($name);
$collection->add_Annotation('header',$comment);
return;
}
return $attribute{$name} unless (defined $value);#get
#print "ATTRIBUTE ",$annot," $name $attribute{$name}\n";
$annot->text($value); #set
return;
}
=head2 chromat_file
Title : chromat_file
Usage : swq->chromat_file([filename]);
Function: Get/Set the CHROMAT_FILE attribute.
Returns : a string if 1 param, nothing else.
Args : none or a filename
=cut
sub Bio::Seq::Quality::chromat_file {
my ($self,$arg) = @_;
return $self->attribute('CHROMAT_FILE',$arg);
}
=head2 abi_thumbprint
Title : abi_thumbprint
Usage : swq->abi_thumbprint([value]);
Function: Get/Set the ABI_THUMBPRINT attribute.
Returns : a string if 1 param, nothing else.
Args : none or a value
=cut
sub Bio::Seq::Quality::abi_thumbprint {
my ($self,$arg) = @_;
return $self->attribute('ABI_THUMBPRINT',$arg);
}
=head2 phred_version
Title : phred_version
Usage : swq->phred_version([value]);
Function: Get/Set the PHRED_VERSION attribute.
Returns : a string if 1 param, nothing else.
Args : none or a value
=cut
sub Bio::Seq::Quality::phred_version {
my ($self,$arg) = @_;
return $self->attribute('PHRED_VERSION', $arg);
}
=head2 call_method
Title : call_method
Usage : swq->call_method([value]);
Function: Get/Set the CALL_METHOD attribute.
Returns : a string if 1 param, nothing else.
Args : none or a value
=cut
sub Bio::Seq::Quality::call_method {
my ($self,$arg) = @_;
return $self->attribute('CALL_METHOD', $arg);
}
=head2 quality_levels
Title : quality_levels
Usage : swq->quality_levels([value]);
Function: Get/Set the quality_levels attribute.
Returns : a string if 1 param, nothing else.
Args : none or a value
=cut
sub Bio::Seq::Quality::quality_levels {
my ($self,$arg) = @_;
return $self->attribute('QUALITY_LEVELS', $arg);
}
=head2 trace_array_min_index
Title : trace_array_min_index
Usage : swq->trace_array_min_index([value]);
Function: Get/Set the trace_array_min_index attribute.
Returns : a string if 1 param, nothing else.
Args : none or a value
=cut
sub Bio::Seq::Quality::trace_array_min_index {
my ($self,$arg) = @_;
return $self->attribute('TRACE_ARRAY_MIN_INDEX', $arg);
}
=head2 trace_array_max_index
Title : trace_array_max_index
Usage : swq->trace_array_max_index([value]);
Function: Get/Set the trace_array_max_index attribute.
Returns : a string if 1 param, nothing else.
Args : none or a value
=cut
sub Bio::Seq::Quality::trace_array_max_index {
my ($self,$arg) = @_;
return $self->attribute('TRACE_ARRAY_MAX_INDEX', $arg);
}
=head2 chem
Title : chem
Usage : swq->chem([value]);
Function: Get/Set the chem attribute.
Returns : a string if 1 param, nothing else.
Args : none or a value
=cut
sub Bio::Seq::Quality::chem {
my ($self,$arg) = @_;
return $self->attribute('CHEM', $arg);
}
=head2 dye
Title : dye
Usage : swq->dye([value]);
Function: Get/Set the dye attribute.
Returns : a string if 1 param, nothing else.
Args : none or a value
=cut
sub Bio::Seq::Quality::dye {
my ($self,$arg) = @_;
return $self->attribute('DYE', $arg);
}
=head2 time
Title : time
Usage : swq->time([value]);
Function: Get/Set the time attribute.
Returns : a string if 1 param, nothing else.
Args : none or a value
=cut
sub Bio::Seq::Quality::time {
my ($self,$arg) = @_;
return $self->attribute('TIME', $arg);
}
=head2 touch
Title : touch
Usage : swq->touch();
Function: Set the time attribute to current time.
Returns : nothing
Args : none
=cut
sub Bio::Seq::Quality::touch {
my $time = localtime();
shift->attribute('TIME',$time);
return;
}
1;