Toolbar

Summary

Bio::SeqIO::pir - PIR sequence input/output stream

Package variables

Included modules

Inherit

Bio::SeqIO

Synopsis

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

Description

This object can transform Bio::Seq objects to and from pir flat
file databases.
Note: This does not completely preserve the PIR format - quality
information about sequence is currently discarded since bioperl
does not have a mechanism for handling these encodings in sequence
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 into the stream
 Returns : 1 for success and 0 for error
 Args    : Array of Bio::PrimarySeqI objects

Methods code

sub _initialize {

  my($self,@args) = @_;
  $self->SUPER::_initialize(@args);    
  if( ! defined $self->sequence_factory ) {
      $self->sequence_factory(new Bio::Seq::SeqFactory
			      (-verbose => $self->verbose(), 
			       -type => 'Bio::Seq'));      
  }

}

sub next_seq {

    my ($self) = @_;
    local $/ = "\n>";
    return unless my $line = $self->_readline;
    if( $line eq '>' ) {	# handle the very first one having no comment
	return unless $line = $self->_readline;
    }
    my ($top, $desc,$seq) = ( $line =~ /^(.+?)\n(.+?)\n([^>]*)/s )  or
	$self->throw("Cannot parse entry PIR entry [$line]");


    my ( $type,$id ) = ( $top =~ /^>?([PF])1;(\S+)\s*$/ ) or
	$self->throw("PIR stream read attempted without leading '>P1;' [ $line ]");

    # P - indicates complete protein
    # F - indicates protein fragment
    # not sure how to stuff these into a Bio object 
    # suitable for writing out.
    $seq =~ s/\*//g;
    $seq =~ s/[\(\)\.\/\=\,]//g;
    $seq =~ s/\s+//g;		# get rid of whitespace

    my ($alphabet) = ('protein');
    # TODO - not processing SFS data
    return $self->sequence_factory->create
	(-seq        => $seq,
	 -primary_id => $id,
	 -id         => $type. '1;' . $id,
	 -desc       => $desc,
	 -alphabet    => $alphabet
	 );

}

sub write_seq {

    my ($self, @seq) = @_;
    for my $seq (@seq) {
	$self->throw("Did not provide a valid Bio::PrimarySeqI object") 
	    unless defined $seq && ref($seq) && $seq->isa('Bio::PrimarySeqI');
	my $str = $seq->seq();
	return unless $self->_print(">".$seq->id(), 
				    "\n", $seq->desc(), "\n", 
				    $str, "*\n");
    }

    $self->flush if $self->_flush_on_write && defined $self->_fh;
    return 1;
}

1;

}

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
  http://www.bioperl.org/MailList.shtml - About the mailing lists

Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution.
Bug reports can be submitted via email or the web:

  bioperl-bugs@bio.perl.org
  http://bugzilla.bioperl.org/

Aaron Mackey <amackey@virginia.edu>
Lincoln Stein <lstein@cshl.org>
Jason Stajich <jason@bioperl.org>

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