bio::seq::largelocatableseq(3pm) [debian man page]

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

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

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