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)