Provided by: libbio-perl-perl_1.7.2-2_all bug


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


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


       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';


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AUTHORS - Jason Stajich



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

        Title   : next_seq
        Usage   : $seq = $stream->next_seq()
        Function: returns the next sequence in the stream
        Returns : A Bio::Seq::LargePrimarySeq 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