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)