NAME¶
Bio::Seq::LargePrimarySeq - PrimarySeq object that stores sequence as files in
the tempdir (as found by File::Temp) or the default method in Bio::Root::Root
SYNOPSIS¶
# normal primary seq usage
DESCRIPTION¶
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 lists
Support¶
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://github.com/bioperl/bioperl-live/issues
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)