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Bio::Tools::Run::Alignment::Blat.3pm
Langue: en
Version: 2009-11-04 (ubuntu - 24/10/10)
Section: 3 (Bibliothèques de fonctions)
Sommaire
NAME
Bio::Tools::Run::Alignment::BlatSYNOPSIS
Build a Blat factory.use Bio::Tools::Run::Alignment::Blat; my $factory = Bio::Tools::Run::Alignment::Blat->new(); # Pass the factory a Bio::Seq object # @feats is an array of Bio::SeqFeature::Generic objects my @feats = $factory->run($seq,$DB);
DESCRIPTION
Wrapper module for Blat programFEEDBACK
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:http://bugzilla.open-bio.org/
AUTHOR - Bala
Email bala@tll.org.sg
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _program_name
Title : program_name Usage : $factory->program_name() Function: holds the program name Returns : string Args : None
program_dir
Title : program_dir Usage : $factory->program_dir(@params) Function: returns the program directory, obtained from ENV variable. Returns : string Args :
new
Title : new Usage : $blat->new(@params) Function: creates a new Blat factory Returns : Bio::Tools::Run::Alignment::Blat Args :
run
Title : run() Usage : $obj->run($query) Function: Runs Blat and creates an array of featrues Returns : An array of Bio::SeqFeature::Generic objects Args : A Bio::PrimarySeqI
align
Title : align Usage : $obj->align($query) Function: Alias to run()
_input
Title : _input Usage : obj->_input($seqFile) Function: Internal (not to be used directly) Returns : Args :
_database
Title : _database Usage : obj->_database($seqFile) Function: Internal (not to be used directly) Returns : Args :
_run
Title : _run Usage : $obj->_run() Function: Internal (not to be used directly) Returns : An array of Bio::SeqFeature::Generic objects Args :
_writeSeqFile
Title : _writeSeqFile Usage : obj->_writeSeqFile($seq) Function: Internal (not to be used directly) Returns : Args :
Contenus ©2006-2024 Benjamin Poulain
Design ©2006-2024 Maxime Vantorre