Bio::SeqIO pir
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Toolbar
WebCvs
Summary
Bio::SeqIO::pir - PIR sequence input/output stream
Package variables
No package variables defined.
Included modules
Bio::Seq::SeqFactory
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
_initialize
No description
Code
next_seqDescriptionCode
write_seqDescriptionCode
Methods description
next_seqcode    nextTop
 Title   : next_seq
Usage : $seq = $stream->next_seq()
Function: returns the next sequence in the stream
Returns : Bio::Seq object
Args : NONE
write_seqcodeprevnextTop
 Title   : write_seq
Usage : $stream->write_seq(@seq)
Function: writes the $seq object into the stream
Returns : 1 for success and 0 for error
Args : Array of Bio::PrimarySeqI objects
Methods code
_initializedescriptionprevnextTop
sub _initialize {
  my($self,@args) = @_;
  $self->SUPER::_initialize(@args);
  if( ! defined $self->sequence_factory ) {
      $self->sequence_factory(Bio::Seq::SeqFactory->new
			      (-verbose => $self->verbose(),
			       -type => 'Bio::Seq'));
  }
}
next_seqdescriptionprevnextTop
sub next_seq {
    my ($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 ); if ( $top =~ /^>?(\S{2});(\S+)\s*$/ ) { ( $type,$id ) = ($1, $2); if (!exists $VALID_TYPE{$type} ) { $self->throw("PIR stream read attempted without proper two-letter sequence code [ $type ]"); } } else { $self->throw("Line does not match PIR format [ $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 => $id, -desc => $desc, -alphabet => $alphabet );
}
write_seqdescriptionprevnextTop
sub write_seq {
    my ($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');

        $self->warn("No whitespace allowed in PIR ID [". $seq->display_id. "]")
            if $seq->display_id =~ /\s/;

	my $str = $seq->seq();
	return unless $self->_print(">P1;".$seq->id(),
				    "\n", $seq->desc(), "\n",
				    $str, "*\n");
    }

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

1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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 Top
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 BugsTop
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/
AUTHORSTop
Aaron Mackey <amackey@virginia.edu>
Lincoln Stein <lstein@cshl.org>
Jason Stajich <jason@bioperl.org>
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _