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 resettable, 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