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Bio::Tools::Run::Profile.3pm
Langue: en
Version: 2009-11-04 (ubuntu - 24/10/10)
Section: 3 (Bibliothèques de fonctions)
Sommaire
NAME
Bio::Tools::Run::ProfileSYNOPSIS
Build a Profile factory # $paramfile is the full path to the seg binary file my @params = ('DB',$dbfile,'PROGRAM',$paramfile); my $factory = Bio::Tools::Run::Profile->new($param); # Pass the factory a Bio::PrimarySeqI object # @feats is an array of Bio::SeqFeature::Generic objects my @feats = $factory->run($seq);
DESCRIPTION
Wrapper module for the pfscan program
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:http://bugzilla.open-bio.org/
AUTHOR - Balamurugan Kumarasamy
Email: fugui@worf.fugu-sg.org
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 : my $factory= Bio::Tools::Run::Profile->new($param); Function: creates a new Profile factory Returns: Bio::Tools::Run::Profile Args :
predict_protein_features
Title : predict_protein_features Usage : DEPRECATED. Use $factory->run($seq) instead. Function: Runs Profile and creates an array of featrues Returns : An array of L<Bio::SeqFeature::FeaturePair> objects Args : A Bio::PrimarySeqI
run
Title : run Usage : my @feats = $factory->run($seq) Function: Runs Profile Returns : An array of L<Bio::SeqFeature::FeaturePair> objects Args : A Bio::PrimarySeqI
_input
Title : _input Usage : $factory->_input($seqFile) Function: get/set for input file Returns : Args :
_run
Title : _run Usage : $factory->_run() Function: Makes a system call and runs pfscan Returns : An array of L<Bio::SeqFeature::FeaturePair> objects Args :
_writeSeqFile
Title : _writeSeqFile Usage : $factory->_writeSeqFile($seq) Function: Creates a file from the given seq object Returns : A string(filename) Args : Bio::PrimarySeqI
Contenus ©2006-2024 Benjamin Poulain
Design ©2006-2024 Maxime Vantorre