Manual Reference Pages - BIO::SEQ::LARGESEQ (3)
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 memory machine!).
Of course, to actually make use of this functionality, the programs
which use this object <B>mustB> 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.
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.
firstname.lastname@example.org - 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
the bugs and their resolution. Bug reports can be submitted via the
AUTHOR - Ewan Birney
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
|perl v5.20.3 ||BIO::SEQ::LARGESEQ (3) ||2016-04-05 |
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