Bio::Seq::LargeSeqI(3pm) User Contributed Perl Documentation Bio::Seq::LargeSeqI(3pm)
NAME
Bio::Seq::LargeSeqI - Interface class for sequences that cache their residues in a temporary file
SYNOPSIS
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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://redmine.open-bio.org/projects/bioperl/
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
perl v5.14.2 2012-03-02 Bio::Seq::LargeSeqI(3pm)