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Bio::Seq::LargePrimaryUser3Contributed Perl DocumeBio::Seq::LargePrimarySeq(3)

NAME
       Bio::Seq::LargePrimarySeq - PrimarySeq object that stores sequence as
       files in	the tempdir (as	found by File::Temp) or	the default method in
       Bio::Root::Root

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://github.com/bioperl/bioperl-live/issues

AUTHOR - Ewan Birney, Jason Stajich
       Email birney@ebi.ac.uk Email jason@bioperl.org

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

   length
	Title	: length
	Usage	:
	Function:
	Example	:
	Returns	:
	Args	:

   seq
	Title	: seq
	Usage	:
	Function:
	Example	:
	Returns	:
	Args	:

   subseq
	Title	: subseq
	Usage	:
	Function:
	Example	:
	Returns	:
	Args	:

   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

   _filename
	Title	: _filename
	Usage	: $obj->_filename($newval)
	Function:
	Example	:
	Returns	: value	of _filename
	Args	: newvalue (optional)

   alphabet
	Title	: alphabet
	Usage	: $obj->alphabet($newval)
	Function:
	Example	:
	Returns	: value	of alphabet
	Args	: newvalue (optional)

perl v5.24.1			  2017-07-08	  Bio::Seq::LargePrimarySeq(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Ewan Birney, Jason Stajich | APPENDIX

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