Bio::Tools::Run::Profile 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); Wrapper module for the pfscan program

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://bio.perl.org/MailList.html - About the mailing lists

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.bioperl.org/ Email: fugui@worf.fugu-sg.org 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, obtiained 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