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)
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Bio::SeqIO::largefasta(3pm) User Contributed Perl Documentation Bio::SeqIO::largefasta(3pm) NAME
Bio::SeqIO::largefasta - method i/o on very large fasta sequence files 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 fasta flat file databases. This module handles very large sequence files by using the Bio::Seq::LargePrimarySeq module to store all the sequence data in a file. This can be a problem if you have limited disk space on your computer because this will effectively cause 2 copies of the sequence file to reside on disk for the life of the Bio::Seq::LargePrimarySeq object. The default location for this is specified by the File::Spec->tmpdir routine which is usually /tmp on UNIX. If a sequence file is larger than the swap space (capacity of the /tmp dir) this could cause problems for the machine. It is possible to set the directory where the temporary file is located by adding the following line to your code BEFORE calling next_seq. See Bio::Seq::LargePrimarySeq for more information. $Bio::Seq::LargePrimarySeq::DEFAULT_TEMP_DIR = 'newdir'; 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 - Jason Stajich Email: jason@bioperl.org 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 : A Bio::Seq::LargePrimarySeq 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 perl v5.14.2 2012-03-02 Bio::SeqIO::largefasta(3pm)