bio::seq::largeseqi(3pm) [debian man page]

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

	#

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)

Check Out this Related Man Page

Bio::SeqIO::ztr(3pm)					User Contributed Perl Documentation				      Bio::SeqIO::ztr(3pm)

NAME

       Bio::SeqIO::ztr - ztr trace sequence input/output stream

SYNOPSIS

       Do not use this module directly.  Use it via the Bio::SeqIO class.

DESCRIPTION

       This object can transform Bio::Seq objects to and from ztr trace files.

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://redmine.open-bio.org/projects/bioperl/

AUTHORS - Aaron Mackey
       Email: amackey@virginia.edu

APPENDIX

       The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

   next_seq
	Title	: next_seq
	Usage	: $seq = $stream->next_seq()
	Function: returns the next sequence in the stream
	Returns : Bio::Seq::Quality object
	Args	: NONE

   write_seq
	Title	: write_seq
	Usage	: $stream->write_seq(@seq)
	Function: writes the $seq object into the stream
	Returns : 1 for success and 0 for error
	Args	: Bio::Seq object

   compression
	Title	: compression
	Usage	: $stream->compression(3);
	Function: determines the level of ZTR compression
	Returns : the current (or newly set) value.
	Args	: 1, 2 or 3 - any other (defined) value will cause the compression
		  to be reset to the default of 2.

perl v5.14.2							    2012-03-02						      Bio::SeqIO::ztr(3pm)

Linux and UNIX Man Pages

bio::seq::largeseqi(3pm) [debian man page]

Check Out this Related Man Page