Bio::Seq::LargeSeq - SeqI compliant object that stores sequence as files in /tmp
# normal primary seq usage
This object 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
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 paste your machine. However,
calls $primary_seq->subseq(10,100) will cause only 90 characters to be
brought into real memory.
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include a thorough description of the problem with code and data examples if
at all possible.
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The rest of the documentation details each of the object methods. Internal
methods are usually preceded with a _
Title : trunc
Usage : $subseq = $myseq->trunc(10,100);
Function: Provides a truncation of a sequence,
Returns : a fresh Bio::SeqI object
Title : add_sequence_as_string
Usage : $seq->add_sequence_as_string("CATGAT");
Function: Appends additional residues to an existing LargePrimarySeq 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