NAME

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

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';

FEEDBACK

   Mailing Lists
       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
       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 Bugs
       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/

AUTHORS - Jason Stajich

       Email: jason@bioperl.org

APPENDIX

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

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

   write_seq
        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