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.

$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