Bio::Tools::PrositeScan

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 AT tll DOT org DOT sg

SEE ALSO

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>.