Bio::Seq::LargeSeq(3pm) 				User Contributed Perl Documentation				   Bio::Seq::LargeSeq(3pm)

NAME

       Bio::Seq::LargeSeq - SeqI compliant object that stores sequence as files in /tmp

SYNOPSIS

	 # normal primary seq usage

DESCRIPTION

       This object stores a sequence as a series of files in a temporary directory. The aim is to allow someone the ability to store very large
       sequences (eg, > 100MBases) in a file system without running out of memory (eg, on a 64 MB real memory machine!).

       Of course, to actually make use of this functionality, the programs which use this object must not call $primary_seq->seq otherwise the
       entire sequence will come out into memory and probably paste your machine. However, calls $primary_seq->subseq(10,100) will cause only 90
       characters to be brought into real memory.

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://redmine.open-bio.org/projects/bioperl/

AUTHOR - Ewan Birney
       Email birney@ebi.ac.uk

APPENDIX

       The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

   trunc
	Title	: trunc
	Usage	: $subseq = $myseq->trunc(10,100);
	Function: Provides a truncation of a sequence,

	Example :
	Returns : a fresh Bio::SeqI object
	Args	:

   Bio::Seq::LargePrimarySeq methods
   add_sequence_as_string
	Title	: add_sequence_as_string
	Usage	: $seq->add_sequence_as_string("CATGAT");
	Function: Appends additional residues to an existing LargePrimarySeq object.
		  This allows one to build up a large sequence without storing
		  entire object in memory.
	Returns : Current length of sequence
	Args	: string to append

perl v5.14.2							    2012-03-02						   Bio::Seq::LargeSeq(3pm)