---
name: "Bio::Tools::PrositeScan"
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::PrositeScan"
---

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

Parser for ps\_scan result

## NAME

Bio::Tools::PrositeScan - Parser for ps\_scan result

## SYNOPSIS

```
  use Bio::Tools::PrositeScan;
  my $factory = Bio::Tools::PrositeScan->new(
      -file   => 'out.PrositeScan',
      -format => 'fasta'
  );
  while(my $match = $factory->next_prediction){
      #  $match is a Bio::SeqFeature::FeaturePair
      # Sequence ID
      my $seq_id = $match->seq_id;
      # PROSITE accession number
      my $psac = $match->hseq_id;
      # Coordinates
      my @coords = ( $match->start, $match->end );
      # Subsequence
      my $seq = $match->feature1->seq;
  }
```

## DESCRIPTION

This is a parser of the output of the ps\_scan program. It takes either a file handle or a file name, and returns a Bio::SeqFeature::FeaturePair object.

Note that the current implementation parses the entire file at once.

## AUTHOR

Juguang Xiao, juguang@tll.org.sg

## SEE ALSO

- •

  ps\_scan software \<ftp://ftp.expasy.org/databases/prosite/ps\_scan\>

- •

  PROSITE User Manual \<http://prosite.expasy.org/prosuser.html\>

### new

```
  Title   : new
  Usage   : Bio::Tools::PrositeScan->new(-file => 'out.PrositeScan');
            Bio::Tools::PrositeScan->new(-fh => \*FH);
  Returns : L<Bio::Tools::PrositeScan>
  Args    : -format => string representing the format type for the
                       ps_scan output, REQUIRED
```

The `"-format"` argument must currently be set to `"fasta"` since this is the only parser implemented. This corresponds with using the ps\_scan arguments `"-o fasta"`.

### next\_prediction

```
  Title   : new
  Usage   :
      while($result = $factory->next_prediction){
          ;
      }
  Returns : a Bio::SeqFeature::FeaturePair object where
            feature1 is the matched subsequence and
            feature2 is the PROSITE accession number.
            See <http://prosite.expasy.org/prosuser.html#conv_ac>.
```