---
name: "Bio::Tools::Run::Profile"
section: "3pm"
platform: "linux"
package: "libbio-perl-run-perl"
version: "1.7.3-13"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/Bio::Tools::Run::Profile"
---

# Bio::Tools::Run::Profile(3pm)

wrapper for the pfscan program

## NAME

Bio::Tools::Run::Profile - wrapper for the pfscan program

## SYNOPSIS

```
 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://redmine.open-bio.org/projects/bioperl/
```

## 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
```