| Bio::Tools::Run::Profile(3pm) | User Contributed Perl Documentation | Bio::Tools::Run::Profile(3pm) |
Bio::Tools::Run::Profile - wrapper for the pfscan program
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
| 2023-01-22 | perl v5.36.0 |