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Bio::Tools::PrositeScaUser Contributed Perl DocumentBio::Tools::PrositeScan(3)

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
       o   ps_scan software <ftp://ftp.expasy.org/databases/prosite/ps_scan>

       o   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>.

perl v5.32.0			  2019-12-07	    Bio::Tools::PrositeScan(3)

NAME | SYNOPSIS | DESCRIPTION | AUTHOR | SEE ALSO

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