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