/ 
FAST-1.06
River stage zero No dependents
/ FAST::Bio::Seq::LargeLocatableSeq

NAME

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

SYNOPSIS

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

DESCRIPTION

FAST::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 FAST::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 = FAST::Bio::Seq::LargeLocatableSeq->new();
Function: Builds a new FAST::Bio::Seq::LargeLocatableSeq object
Returns : an instance of FAST::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)