Bio::SeqIO::largefasta(3pm)				User Contributed Perl Documentation			       Bio::SeqIO::largefasta(3pm)

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

perl v5.14.2							    2012-03-02					       Bio::SeqIO::largefasta(3pm)