bio::seq::largeseq(3pm) [debian man page]
Bio::Seq::LargeSeq(3pm) User Contributed Perl Documentation Bio::Seq::LargeSeq(3pm) NAME
Bio::Seq::LargeSeq - SeqI compliant object that stores sequence as files in /tmp SYNOPSIS
# normal primary seq usage DESCRIPTION
This object stores a sequence as a series of files in a temporary directory. The aim is to allow someone the ability to store very large sequences (eg, > 100MBases) in a file system without running out of memory (eg, on a 64 MB real memory machine!). Of course, to actually make use of this functionality, the programs which use this object must not call $primary_seq->seq otherwise the entire sequence will come out into memory and probably paste your machine. However, calls $primary_seq->subseq(10,100) will cause only 90 characters to be brought into real memory. 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/ AUTHOR - Ewan Birney Email birney@ebi.ac.uk APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ trunc Title : trunc Usage : $subseq = $myseq->trunc(10,100); Function: Provides a truncation of a sequence, Example : Returns : a fresh Bio::SeqI object Args : Bio::Seq::LargePrimarySeq methods add_sequence_as_string Title : add_sequence_as_string Usage : $seq->add_sequence_as_string("CATGAT"); Function: Appends additional residues to an existing LargePrimarySeq 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::LargeSeq(3pm)
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Bio::Seq::LargeLocatableSeq(3pm) User Contributed Perl Documentation Bio::Seq::LargeLocatableSeq(3pm) NAME
Bio::Seq::LargeLocatableSeq - LocatableSeq object that stores sequence as files in the tempdir SYNOPSIS
# normal primary seq usage use Bio::Seq::LargeLocatableSeq; my $seq = Bio::Seq::LargeLocatableSeq->new(-seq => "CAGT-GGT", -id => "seq1", -start => 1, -end => 7); DESCRIPTION
Bio::Seq::LargeLocatableSeq - object with start/end points on it that can be projected into a MSA or have coordinates relative to another seq. This object, unlike Bio::LocatableSeq, stores a sequence as a series of files in a temporary directory. The aim is to allow someone the ability to store very large sequences (eg, > 100MBases) in a file system without running out of memory (eg, on a 64 MB real memory machine!). Of course, to actually make use of this functionality, the programs which use this object must not call $primary_seq->seq otherwise the entire sequence will come out into memory and probably crash your machine. However, calls like $primary_seq->subseq(10,100) will cause only 90 characters to be brought into real memory. 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 the web: https://redmine.open-bio.org/projects/bioperl/ AUTHOR - Albert Vilella Email avilella-AT-gmail-DOT-com APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ new Title : new Usage : my $obj = Bio::Seq::LargeLocatableSeq->new(); Function: Builds a new Bio::Seq::LargeLocatableSeq object Returns : an instance of Bio::Seq::LargeLocatableSeq Args : length Title : length Usage : Function: Example : Returns : Args : seq Title : seq Usage : Function: Example : Returns : Args : subseq Title : subseq Usage : Function: Example : Returns : Args : add_sequence_as_string Title : add_sequence_as_string Usage : $seq->add_sequence_as_string("CATGAT"); Function: Appends additional residues to an existing LargeLocatableSeq 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 _filename Title : _filename Usage : $obj->_filename($newval) Function: Example : Returns : value of _filename Args : newvalue (optional) alphabet Title : alphabet Usage : $obj->alphabet($newval) Function: Example : Returns : value of alphabet Args : newvalue (optional) perl v5.14.2 2012-03-02 Bio::Seq::LargeLocatableSeq(3pm)