Bio::SeqIO::phd - phd file input/output stream

BioPerl documentation Contained in the BioPerl distribution.

Index

Code Index:

NAME

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Bio::SeqIO::phd - phd file input/output stream

SYNOPSIS

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Do not use this module directly. Use it via the Bio::SeqIO class.

DESCRIPTION

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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

FEEDBACK

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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

Support

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

AUTHOR Chad Matsalla

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Chad Matsalla bioinformatics@dieselwurks.com

CONTRIBUTORS

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Jason Stajich, jason@bioperl.org Jean-Marc Frigerio, Frigerio@pierroton.inra.fr

APPENDIX

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

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

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

write_seq

 Title   : write_seq()
 Usage   : $seqio->write_seq($swq);
 Function: Write out a phd file.
 Returns : Nothing.
 Args    : a Bio::Seq::Quality object

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

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

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

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

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

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

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

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

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

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

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

touch

 Title   : touch
 Usage   : swq->touch();
 Function: Set the time attribute to current time.
 Returns : nothing
 Args    : none
BioPerl documentation Contained in the BioPerl distribution. 
#
# 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


# '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 = new Dumpvalue();

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'));
  }
}


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;
}



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;
}


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;
}


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;
}



sub Bio::Seq::Quality::chromat_file {
    my ($self,$arg) =  @_;
    return $self->attribute('CHROMAT_FILE',$arg);
}


sub Bio::Seq::Quality::abi_thumbprint {
    my ($self,$arg) =  @_;
    return $self->attribute('ABI_THUMBPRINT',$arg);
}



sub Bio::Seq::Quality::phred_version {
    my ($self,$arg) =  @_;
    return $self->attribute('PHRED_VERSION', $arg);
   }



sub Bio::Seq::Quality::call_method {
    my ($self,$arg) =  @_;
    return $self->attribute('CALL_METHOD', $arg);
    }


sub Bio::Seq::Quality::quality_levels {
    my ($self,$arg) =  @_;
    return $self->attribute('QUALITY_LEVELS', $arg);
    }


sub Bio::Seq::Quality::trace_array_min_index {
    my ($self,$arg) =  @_;
    return $self->attribute('TRACE_ARRAY_MIN_INDEX', $arg);
 }


sub Bio::Seq::Quality::trace_array_max_index {
    my ($self,$arg) =  @_;
    return $self->attribute('TRACE_ARRAY_MAX_INDEX', $arg);
}


sub Bio::Seq::Quality::chem {
    my ($self,$arg) =  @_;
    return $self->attribute('CHEM', $arg);
}


sub Bio::Seq::Quality::dye {
    my ($self,$arg) =  @_;
    return $self->attribute('DYE', $arg);
}


sub Bio::Seq::Quality::time {
    my ($self,$arg) =  @_;
    return $self->attribute('TIME', $arg);
}


sub Bio::Seq::Quality::touch {
    my $time = localtime();
    shift->attribute('TIME',$time);
    return;
}

1;