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Bio::SeqIO::largefastaUser Contributed Perl DocumentaBio::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
       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

perl v5.24.1			  2017-07-08	     Bio::SeqIO::largefasta(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHORS - Jason Stajich | APPENDIX

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