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
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : program_name Usage : $factory>program_name() Function: holds the program name Returns: string Args : None
Title : program_dir Usage : $factory->program_dir(@params) Function: returns the program directory, obtained from ENV variable. Returns: string Args :
Title : new Usage : my $factory= Bio::Tools::Run::Profile->new($param); Function: creates a new Profile factory Returns: Bio::Tools::Run::Profile Args :
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
Title : run Usage : my @feats = $factory->run($seq) Function: Runs Profile Returns : An array of L<Bio::SeqFeature::FeaturePair> objects Args : A Bio::PrimarySeqI
Title : _input Usage : $factory->_input($seqFile) Function: get/set for input file Returns : Args :
Title : _run Usage : $factory->_run() Function: Makes a system call and runs pfscan Returns : An array of L<Bio::SeqFeature::FeaturePair> objects Args :
Title : _writeSeqFile Usage : $factory->_writeSeqFile($seq) Function: Creates a file from the given seq object Returns : A string(filename) Args : Bio::PrimarySeqI