---
name: "Bio::Matrix::PSM::IO::transfac"
section: "3pm"
platform: "linux"
package: "libbio-perl-perl"
version: "1.7.8-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/Bio::Matrix::PSM::IO::transfac"
---

# Bio::Matrix::PSM::IO::transfac(3pm)

PSM transfac parser

## NAME

Bio::Matrix::PSM::IO::transfac - PSM transfac parser

## SYNOPSIS

See Bio::Matrix::PSM::IO for documentation

## DESCRIPTION

\#

## 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:

```
  https://github.com/bioperl/bioperl-live/issues
```

## AUTHOR - Stefan Kirov

Email skirov@utk.edu

## APPENDIX

### new

```
 Title   : new
 Usage   : my $psmIO =  Bio::Matrix::PSM::IO->new(-format=>'transfac',
                                                 -file=>$file);
 Function: Associates a file with the appropriate parser
 Throws  :
 Example :
 Args    :
 Returns : "Bio::Matrix::PSM::$format"->new(@args);
```

### next\_psm

```
 Title   : next_psm
 Usage   : my $psm=$psmIO->next_psm();
 Function: Reads the next PSM from the input file, associated with this object
 Throws  : Upon finding a line, defining the matrix, where one or more positions
            are not defined, see _make_matrix
 Returns : Bio::Matrix::PSM::Psm object
 Args    : none
```

### \_parseMatrix

```
 Title   : _parseMatrix
 Usage   :
 Function: Parses a line
 Throws  :
 Example :  Internal stuff
 Returns :  array (frequencies for A,C,G,T in this order).
 Args    :  string
```

### \_make\_matrix

```
 Title   : _make_matrix
 Usage   :
 Function:
 Throws  :  If a position is undefined, for example if you have line like this
            in the file you are parsing: 08  4,7,,9
 Example :  Internal stuff
 Returns :
 Args    :
```