---
name: "Bio::Tools::Run::Pseudowise"
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::Pseudowise"
---

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

Object for prediting pseudogenes in a given sequence given a protein and a cdna sequence

## NAME

Bio::Tools::Run::Pseudowise - Object for prediting pseudogenes in a given sequence given a protein and a cdna sequence

## SYNOPSIS

```
  # Build a pseudowise alignment factory
  my $factory = Bio::Tools::Run::Pseudowise->new();
  # Pass the factory 3 Bio:SeqI objects (in the order of query
  # peptide and cdna and target_genomic)
  # @genes is an array of GenericSeqFeature objects
  my @genes = $factory->run($seq1, $seq2, $seq3);
```

## DESCRIPTION

Pseudowise is a pseudogene predition program developed by Ewan Birney http://www.sanger.ac.uk/software/wise2.

## 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 - Kiran

Email kiran@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    :
```

### version

```
 Title   : version
 Usage   : exit if $prog->version() < 1.8
 Function: Determine the version number of the program
 Example :
 Returns : float or undef
 Args    : none
```

### predict\_genes

```
 Title   : predict_genes
 Usage   : DEPRECATED. Use $factory->run instead
 Function: Predict pseudogenes
 Returns : An array of Bio::Seqfeature::Generic objects
 Args    : Name of a file containing a set of 3 fasta sequences in the order of
           peptide, cdna and genomic sequences
           or else 3  Bio::Seq objects.
```

Throws an exception if argument is not either a string (eg a filename) or 3 Bio::Seq objects.  If arguments are strings, throws exception if file corresponding to string name can not be found.

### run

```
 Title   : run
 Usage   : my @feats = $factory->run($seq1, $seq2, $seq3);
 Function: Executes pseudogene binary
 Returns : An array of Bio::Seqfeature::Generic objects
 Args    : Name of a file containing a set of 3 fasta sequences in the order of
           peptide, cdna and genomic sequences
           or else 3  Bio::Seq objects.
```

Throws an exception if argument is not either a string (eg a filename) or 3 Bio::Seq objects.  If arguments are strings, throws exception if file corresponding to string name can not be found.

### \_run

```
 Title   :  _run
 Usage   :  Internal function, not to be called directly
 Function:   makes actual system call to a pseudowise program
 Example :
 Returns : nothing; pseudowise  output is written to a
           temporary file $TMPOUTFILE
 Args    : Name of a files containing 3 sequences in the order of peptide, cdna and genomic
```

### \_parse\_results

```
 Title   :  __parse_results
 Usage   :  Internal function, not to be called directly
 Function:  Parses pseudowise output
 Example :
 Returns : an reference to an array of Seqfeatures
 Args    : the name of the output file
```

### \_setinput()

```
 Title   :  _setinput
 Usage   :  Internal function, not to be called directly
 Function:   Create input files for pseudowise program
 Example :
 Returns : name of file containing dba data input
 Args    : Seq objects in the order of query protein and cdna and target genomic sequence
```

### \_query\_pep\_seq()

```
 Title   :  _query_pep_seq
 Usage   :  Internal function, not to be called directly
 Function:  get/set for the query sequence
 Example :
 Returns :
 Args    :
```

### \_query\_cdna\_seq()

```
 Title   :  _query_cdna_seq
 Usage   :  Internal function, not to be called directly
 Function:  get/set for the query sequence
 Example :
 Returns :
 Args    :
```

### \_subject\_dna\_seq()

```
 Title   :  _subject_dna_seq
 Usage   :  Internal function, not to be called directly
 Function:  get/set for the subject sequence
 Example :
 Returns :
 Args    :
```