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.\" ========================================================================
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.IX Title "Bio::Tools::PrositeScan 3pm"
.TH Bio::Tools::PrositeScan 3pm "2021-08-15" "perl v5.32.1" "User Contributed Perl Documentation"
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.SH "NAME"
Bio::Tools::PrositeScan \- Parser for ps_scan result
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 1
\&  use Bio::Tools::PrositeScan;
\&
\&  my $factory = Bio::Tools::PrositeScan\->new(
\&      \-file   => \*(Aqout.PrositeScan\*(Aq,
\&      \-format => \*(Aqfasta\*(Aq
\&  );
\&
\&  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;
\&  }
.Ve
.SH "DESCRIPTION"
.IX Header "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.
.PP
Note that the current implementation parses the entire file at once.
.SH "AUTHOR"
.IX Header "AUTHOR"
Juguang Xiao, juguang@tll.org.sg
.SH "SEE ALSO"
.IX Header "SEE ALSO"
.IP "\(bu" 4
ps_scan software <ftp://ftp.expasy.org/databases/prosite/ps_scan>
.IP "\(bu" 4
\&\s-1PROSITE\s0 User Manual <http://prosite.expasy.org/prosuser.html>
.SS "new"
.IX Subsection "new"
.Vb 6
\&  Title   : new
\&  Usage   : Bio::Tools::PrositeScan\->new(\-file => \*(Aqout.PrositeScan\*(Aq);
\&            Bio::Tools::PrositeScan\->new(\-fh => \e*FH);
\&  Returns : L<Bio::Tools::PrositeScan>
\&  Args    : \-format => string representing the format type for the
\&                       ps_scan output, REQUIRED
.Ve
.PP
The \f(CW\*(C`\-format\*(C'\fR argument must currently be set to \f(CW\*(C`fasta\*(C'\fR since this is the
only parser implemented. This corresponds with using the ps_scan arguments
\&\f(CW\*(C`\-o fasta\*(C'\fR.
.SS "next_prediction"
.IX Subsection "next_prediction"
.Vb 5
\&  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>.
.Ve