Provided by: libbio-perl-perl_1.7.2-2_all bug

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>.