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Summary

Bio::SeqIO::swissdriver - SwissProt/UniProt handler-based push parser

Package variables

Included modules

Inherit

Bio::SeqIO

Synopsis

  #It is probably best not to use this object directly, but
  #rather go through the SeqIO handler:

  $stream = Bio::SeqIO->new(-file => $filename,
                            -format => 'swissdriver');

  while ( my $seq = $stream->next_seq() ) {
      # do something with $seq
  }

Description

This object can transform Bio::Seq objects to and from UniProt flat file
databases. The key difference between this parser and the tried-and-true
Bio::SeqIO::swiss parser is this version separates the parsing and data
manipulation into a 'driver' method (next_seq) and separate object handlers
which deal with the data passed to it. The main purpose of the driver routine, in this case next_seq(), is to carve out
the data into meaningful chunks which are passed along to relevant handlers (see
below).
Each chunk of data in the has a NAME tag attached to it, similar to that for XML
parsing. This designates the type of data passed (annotation type or seqfeature)
and the handler to be called for processing the data.

Methods

Methods description

 Title   : next_seq
 Usage   : $seq = $stream->next_seq()
 Function: returns the next sequence in the stream
 Returns : Bio::Seq object
 Args    : none

 Title   : write_seq
 Usage   : $stream->write_seq($seq)
 Function: writes the $seq object (must be seq) to the stream
 Returns : 1 for success and 0 for error
 Args    : array of 1 to n Bio::SeqI objects

 Title   : seqhandler
 Usage   : $stream->seqhandler($handler)
 Function: Get/Set teh Bio::Seq::HandlerBaseI object
 Returns : Bio::Seq::HandlerBaseI 
 Args    : Bio::Seq::HandlerBaseI

Methods code

sub _initialize {

    my($self,@args) = @_;

    $self->SUPER::_initialize(@args);
    my $handler = $self->_rearrange([qw(HANDLER)],@args);
    # hash for functions for decoding keys.
    $handler ? $self->seqhandler($handler) :
    $self->seqhandler(Bio::SeqIO::Handler::GenericRichSeqHandler->new(
                    -format => 'swiss',
                    -verbose => $self->verbose,
                    -builder => $self->sequence_builder
                    ));
    if( ! defined $self->sequence_factory ) {
        $self->sequence_factory(Bio::Seq::SeqFactory->new
                (-verbose => $self->verbose(),
                 -type => 'Bio::Seq::RichSeq'));
    }

}

sub next_seq {

    my $self = shift;
    my $hobj = $self->seqhandler;
    local($/) = "\n";
    # these contain values that need to carry over each round
    my ($featkey, $qual, $annkey, $seqdata, $location);
    my $lastann = '';
    my $ct = 0;
    # main parser
    PARSER:
    while(defined(my $line = $self->_readline)) {
        chomp $line;
        my ($ann, $data) = split(m{\s+}, $line, 2);
        if ($ann) {
            if ($ann eq 'FT') {
                # sequence features
                if ($data =~ m{^(\w+)\s+([\d\?\<]+)\s+([\d\?\>]+)(?:\s+?(\S.*))?}ox) {
                    # has location data and desc
                    if ($seqdata) {
                        $hobj->data_handler($seqdata);
                        $seqdata = ();
                    }
                    ($seqdata->{FEATURE_KEY}, my $loc1, my $loc2, $data) = ($1, $2, $3, $4);
                    $qual = 'description';
                    $seqdata->{$qual} = $data;
                    $seqdata->{NAME} = $ann;
                    $seqdata->{LOCATION} = "$loc1..$loc2" if defined $loc1;
                    next PARSER;
                } elsif ($data =~ m{^\s+/([^=]+)(?:=(.+))?}ox) {
                    # has qualifer
                    ($qual, $data) = ($1, $2 || '');
                    $ct = ($seqdata->{$qual}) ? 
                        ((ref($seqdata->{$qual}))  ? scalar(@{ $seqdata->{$qual} }) : 1)
                        : 0 ;
                }
                $data =~ s{\.$}{};
                if ($ct == 0) {
                    $seqdata->{$qual} .= ($seqdata->{$qual}) ?
                        ' '.$data : $data;                    
                } else {
                    if (!ref($seqdata->{$qual})) {
                        $seqdata->{$qual} = [$seqdata->{$qual}];
                    }
                    ($seqdata->{$qual}->[$ct]) ?
                        ($seqdata->{$qual}->[$ct] .= ' '.$data) :
                        ($seqdata->{$qual}->[$ct] .= $data);
                }
            } else {
                # simple annotations
                if ($ann ne $lastann) {
                    if (!$SEC{$ann} && $seqdata) {
                        $hobj->data_handler($seqdata);
                        # can't use undef here; it can lead to subtle mem leaks
                        $seqdata = ();
                    }
                    $annkey = (!$SEC{$ann})    ? 'DATA'     : # primary data
                              $SEC{$ann};
                    $seqdata->{'NAME'} = $ann if !$SEC{$ann};
                }
                last PARSER if $ann eq '//';
                next PARSER if $ann eq 'SQ';
                my $delim = $DELIM{$ann} || ' ';
                $seqdata->{$annkey} .= ($seqdata->{$annkey}) ?
                    $delim.$data : $data;
                $lastann = $ann;
            } 
        } else {
            # this should only be sequence (fingers crossed!)
            SEQUENCE:
            while (defined ($line = $self->_readline)) {
                if (index($line, '//') == 0) {
                    $data =~ tr{0-9 \n}{}d;
                    $seqdata->{DATA} = $data;
                    #$self->debug(Dumper($seqdata));
                    $hobj->data_handler($seqdata);
                    $seqdata = ();
                    last PARSER;
                } else {                        
                    $data .= $line;
                    $line = undef;
                }
            }
        }
    }
    # some files have no // for the last file; this catches the last bit o' data
    $hobj->data_handler($seqdata) if $seqdata;
    return $hobj->build_sequence;

}

sub write_seq {

    shift->throw("Use Bio::SeqIO::swiss write_seq() for output");
    # maybe make a Writer class as well????

}

sub seqhandler {

    my ($self, $handler) = @_;
    if ($handler) {
        $self->throw("Not a Bio::HandlerBaseI") unless
        ref($handler) && $handler->isa("Bio::HandlerBaseI");
        $self->{'_seqhandler'} = $handler;
    }
    return $self->{'_seqhandler'};
}

1;

__END__

}

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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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.

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/

bioperl-l at bioperl.org

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