Bio::Tools::PrositeScan(3pm)

Usage

  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;
  }

Overview

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.

Releases

9 releases since Debian 5.0 (Lenny); the text changed 7 times.

5.0
6.0
7
8
9
10
11
12–13