Bio::SeqIO::largefasta(3)

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 the Bio::Seq::LargePrimarySeq manpage 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 the Bio::Seq::LargePrimarySeq manpage object. The default location for this is specified by the the File::Spec manpage->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.

    $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/MailList.shtml - About the mailing lists

  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 email or the web:

  bioperl-bugs@bio.perl.org
  http://bio.perl.org/bioperl-bugs/

AUTHORS - Jason Stajich
Email: jason@chg.mc.duke.edu

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 : Bio::Seq object
 Args    : NONE

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