xenial (3) Bio::SeqIO::largefasta.3pm.gz

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://github.com/bioperl/bioperl-live/issues

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