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.
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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)