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

• PROSITE User Manual

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>.