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Bio::Seq::LargeLocatabUserqContributed Perl DocuBio::Seq::LargeLocatableSeq(3)

NAME
       Bio::Seq::LargeLocatableSeq - LocatableSeq object that stores sequence
       as files	in the tempdir

SYNOPSIS
	 # normal primary seq usage
	   use Bio::Seq::LargeLocatableSeq;
	   my $seq = Bio::Seq::LargeLocatableSeq->new(-seq => "CAGT-GGT",
						     -id  => "seq1",
						     -start => 1,
						     -end   => 7);

DESCRIPTION
       Bio::Seq::LargeLocatableSeq - object with start/end points on it	that
       can be projected	into a MSA or have coordinates relative	to another
       seq.

       This object, unlike Bio::LocatableSeq, 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 crash your
       machine.	However, calls like $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 the
       Bioperl mailing list.  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 of
       the bugs	and their resolution. Bug reports can be submitted via the
       web:

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

AUTHOR - Albert	Vilella
       Email avilella-AT-gmail-DOT-com

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

   new
	Title	: new
	Usage	: my $obj = Bio::Seq::LargeLocatableSeq->new();
	Function: Builds a new Bio::Seq::LargeLocatableSeq object
	Returns	: an instance of Bio::Seq::LargeLocatableSeq
	Args	:

   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 LargeLocatableSeq 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::LargeLocatableSeq(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Albert Vilella | APPENDIX

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