NAME¶
Bio::Seq::LargeSeqI - Interface class for sequences that cache their residues in
a temporary file
SYNOPSIS¶
#
DESCRIPTION¶
The interface class defines a group of sequence classes that do not keep their
sequence information in memory but store it in a file. This makes it possible
to work with very large files even with limited RAM.
The most important consequence of file caching for sequences is that you do not
want to inspect the sequence unless absolutely necessary. These sequences
typically override the
length() method not to check the sequence.
The
seq() method is not resetable, if you want to add to the end of the
sequence you have to use
add_sequence_as_string(), for any other
sequence changes you'll have to create a new object.
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 the Bioperl mailing
list. 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 of the bugs
and their resolution. Bug reports can be submitted via email or the web:
https://github.com/bioperl/bioperl-live/issues
AUTHOR - Albert Vilella¶
Email avilella-AT-gmail-DOT-com
CONTRIBUTORS¶
Heikki Lehvaslaiho, heikki-at-bioperl-dot-org
APPENDIX¶
The rest of the documentation details each of the object methods. Internal
methods are usually preceded with a _
add_sequence_as_string¶
Title : add_sequence_as_string
Usage : $seq->add_sequence_as_string("CATGAT");
Function: Appends additional residues to an existing 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