NAME
FAST::Bio::Seq::LargePrimarySeq - PrimarySeq object that stores sequence as files in the tempdir (as found by File::Temp) or the default method in FAST::Bio::Root::Root
SYNOPSIS
# normal primary seq usageDESCRIPTION
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 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.
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 one of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing listsSupport
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 the bugs and their resolution. Bug reports can be submitted via the web:
https://redmine.open-bio.org/projects/bioperl/AUTHOR - Ewan Birney, Jason Stajich
Email birney@ebi.ac.uk Email jason@bioperl.org
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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 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_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)