Bio::Seq::LargeLocatabUserqContributed Perl DocuBio::Seq::LargeLocatableSeq(3)NAMEBio::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);
DESCRIPTIONBio::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:
http://bugzilla.open-bio.org/
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 v5.14.1 2011-07-22 Bio::Seq::LargeLocatableSeq(3)
