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Summary

Bio::SeqIO::largefasta - method i/o on very large fasta sequence files

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 fasta flat
file databases.
This module handles very large sequence files by using the
Bio::Seq::LargePrimarySeq module to store all the sequence data in
a file. This can be a problem if you have limited disk space on your
computer because this will effectively cause 2 copies of the sequence
file to reside on disk for the life of the
Bio::Seq::LargePrimarySeq object. The default location for this is
specified by the File::Spec->tmpdir routine which is usually /tmp
on UNIX. If a sequence file is larger than the swap space (capacity
of the /tmp dir) this could cause problems for the machine. It is
possible to set the directory where the temporary file is located by
adding the following line to your code BEFORE calling next_seq. See
Bio::Seq::LargePrimarySeq for more information.

    $Bio::Seq::LargePrimarySeq::DEFAULT_TEMP_DIR = 'newdir';

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    : Bio::Seq object

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::LargePrimarySeq'));      
  }

}

sub next_seq {

    my ($self) = @_;
#  local $/ = "\n";
    my $largeseq = $self->sequence_factory->create();
    my ($id,$fulldesc,$entry);
    my $count = 0;
    my $seen = 0;
    while( defined ($entry = $self->_readline) ) {
	if( $seen == 1 && $entry =~ /^\s*>/ ) {
	    $self->_pushback($entry);
	    return $largeseq;
	}
#	if ( ($entry eq '>') || eof($self->_fh) ) { $seen = 1; next; }      
	if ( ($entry eq '>')  ) { $seen = 1; next; }      
	elsif( $entry =~ /\s*>(.+?)$/ ) {
	    $seen = 1;
	    ($id,$fulldesc) = ($1 =~ /^\s*(\S+)\s*(.*)$/)
		or $self->warn("Can't parse fasta header");
	    $largeseq->display_id($id);
	    $largeseq->primary_id($id);	  
	    $largeseq->desc($fulldesc);
	} else {
	    $entry =~ s/\s+//g;
	    $largeseq->add_sequence_as_string($entry);
	}
	(++$count % 1000 == 0 && $self->verbose() > 0) && print "line $count\n";
    }
    if( ! $seen ) { return undef; } 
    return $largeseq;

}

sub write_seq {

   my ($self,@seq) = @_;
   foreach my $seq (@seq) {       
     my $top = $seq->id();
     if ($seq->can('desc') and my $desc = $seq->desc()) {
	 $desc =~ s/\n//g;
	 $top .= " $desc";
     }
     $self->_print (">",$top,"\n");
     my $end = $seq->length();
     my $start = 1;
     while( $start < $end ) {
	 my $stop = $start + $FASTALINELEN - 1;
	 $stop = $end if( $stop > $end );
	 $self->_print($seq->subseq($start,$stop), "\n");
	 $start += $FASTALINELEN;
     }
   }

   $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://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/

Email: jason@bioperl.org

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