Bio::Seq::LargeLocatableSeq - LocatableSeq object that stores sequence as files in the tempdir
# normal primary seq usage use Bio::Seq::LargeLocatableSeq; my $seq = Bio::Seq::LargeLocatableSeq->new(-seq => "CAGT-GGT", -id => "seq1", -start => 1, -end => 7);
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.
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.
email@example.com - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Please direct usage questions or support issues to the mailing list:
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.
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:
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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 :
Title : length Usage : Function: Example : Returns : Args :
Title : seq Usage : Function: Example : Returns : Args :
Title : subseq Usage : Function: Example : Returns : Args :
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
Title : _filename Usage : $obj->_filename($newval) Function: Example : Returns : value of _filename Args : newvalue (optional)
Title : alphabet Usage : $obj->alphabet($newval) Function: Example : Returns : value of alphabet Args : newvalue (optional)