---
name: "Bio::Tools::Genscan"
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::Tools::Genscan"
---

# Bio::Tools::Genscan(3pm)

Results of one Genscan run

## NAME

Bio::Tools::Genscan - Results of one Genscan run

## SYNOPSIS

```
   use Bio::Tools::Genscan;
   $genscan = Bio::Tools::Genscan->new(-file => 'result.genscan');
   # filehandle:
   $genscan = Bio::Tools::Genscan->new( -fh  => \*INPUT );
   # parse the results
   # note: this class is-a Bio::Tools::AnalysisResult which implements
   # Bio::SeqAnalysisParserI, i.e., $genscan->next_feature() is the same
   while($gene = $genscan->next_prediction()) {
       # $gene is an instance of Bio::Tools::Prediction::Gene, which inherits
       # off Bio::SeqFeature::Gene::Transcript.
       #
       # $gene->exons() returns an array of
       # Bio::Tools::Prediction::Exon objects
       # all exons:
       @exon_arr = $gene->exons();
       # initial exons only
       @init_exons = $gene->exons('Initial');
       # internal exons only
       @intrl_exons = $gene->exons('Internal');
       # terminal exons only
       @term_exons = $gene->exons('Terminal');
       # singleton exons:
       ($single_exon) = $gene->exons();
   }
   # essential if you gave a filename at initialization (otherwise the file
   # will stay open)
   $genscan->close();
```

## DESCRIPTION

The Genscan module provides a parser for Genscan gene structure prediction output. It parses one gene prediction into a Bio::SeqFeature::Gene::Transcript- derived object.

This module also implements the Bio::SeqAnalysisParserI interface, and thus can be used wherever such an object fits. See Bio::SeqAnalysisParserI.

## 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 - Hilmar Lapp

Email hlapp@gmx.net

## APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a \_

### analysis\_method

```
 Usage     : $genscan->analysis_method();
 Purpose   : Inherited method. Overridden to ensure that the name matches
             /genscan/i.
 Returns   : String
 Argument  : n/a
```

### next\_feature

```
 Title   : next_feature
 Usage   : while($gene = $genscan->next_feature()) {
                  # do something
           }
 Function: Returns the next gene structure prediction of the Genscan result
           file. Call this method repeatedly until FALSE is returned.
           The returned object is actually a SeqFeatureI implementing object.
           This method is required for classes implementing the
           SeqAnalysisParserI interface, and is merely an alias for
           next_prediction() at present.
 Example :
 Returns : A Bio::Tools::Prediction::Gene object.
 Args    :
```

### next\_prediction

```
 Title   : next_prediction
 Usage   : while($gene = $genscan->next_prediction()) {
                  # do something
           }
 Function: Returns the next gene structure prediction of the Genscan result
           file. Call this method repeatedly until FALSE is returned.
 Example :
 Returns : A Bio::Tools::Prediction::Gene object.
 Args    :
```

### \_parse\_predictions

```
 Title   : _parse_predictions()
 Usage   : $obj->_parse_predictions()
 Function: Parses the prediction section. Automatically called by
           next_prediction() if not yet done.
 Example :
 Returns :
```

### \_prediction

```
 Title   : _prediction()
 Usage   : $gene = $obj->_prediction()
 Function: internal
 Example :
 Returns :
```

### \_add\_prediction

```
 Title   : _add_prediction()
 Usage   : $obj->_add_prediction($gene)
 Function: internal
 Example :
 Returns :
```

### \_predictions\_parsed

```
 Title   : _predictions_parsed
 Usage   : $obj->_predictions_parsed
 Function: internal
 Example :
 Returns : TRUE or FALSE
```

### \_has\_cds

```
 Title   : _has_cds()
 Usage   : $obj->_has_cds()
 Function: Whether or not the result contains the predicted CDSs, too.
 Example :
 Returns : TRUE or FALSE
```

### \_read\_fasta\_seq

```
 Title   : _read_fasta_seq()
 Usage   : ($id,$seqstr) = $obj->_read_fasta_seq();
 Function: Simple but specialised FASTA format sequence reader. Uses
           $self->_readline() to retrieve input, and is able to strip off
           the traling description lines.
 Example :
 Returns : An array of two elements.
```