view release on metacpan or  search on metacpan

Bio/Tools/Protparam.pm  view on Meta::CPAN

	"Composition of W : ", $pp->AA_comp('W'),"\n",
	"Composition of Y : ", $pp->AA_comp('Y'),"\n",
	"Composition of V : ", $pp->AA_comp('V'),"\n",
	"Composition of B : ", $pp->AA_comp('B'),"\n",
	"Composition of Z : ", $pp->AA_comp('Z'),"\n",
	"Composition of X : ", $pp->AA_comp('X'),"\n";
}

=head1 DESCRIPTION

This module takes an amino acid sequence and submits it to the
Protparam program at www.expasy.org/cgi-bin/protparam.  Many
properties of the submitted sequence are returned.

=head1 AUTHOR

Richard Dobson, r.j.dobson at qmul dot ac dot uk

=cut

# Let the code begin...

package Bio::Tools::Protparam;

use strict;
use base qw(Bio::Root::Root);
use LWP 5.64;

=head2 new

  Title    : new
  Usage    : $pp = Protparam->new(seq=>$seq->seq);
  Function : Creates a new Protparam object
  Returns  : A Protparam object
  Args     : A sequence

=cut

sub new {
	my ($class,@args) = @_;
	@args=('-url'=>'http://web.expasy.org/cgi-bin/protparam/protparam','-form'=>'sequence',@args);
	my $self=$class->SUPER::new(@args);

	my ($url,$seq,$form)=$self->_rearrange([qw(URL SEQ FORM)],@args);

	my $browser = LWP::UserAgent->new;
	my $response;

	#send request to PROTPARAM @ Expasy
	$response = $browser->post($url,
                           [
                            $form => $seq
                           ],
                           'User-Agent' => 'Mozilla/4.76 [en] (Win2000; U)',
                          );

	#Check if successful
	$self->throw("$url error: ".$response->status_line) unless $response->is_success;
	$self->throw("Bad content type at $url ".$response->content_type) unless $response->content_type eq 'text/html';

	my $protParamOutput=$response->decoded_content;

	$self->{'output'}=$protParamOutput;

	return bless $self,$class;

}

=head2 num_neg

  Title    : num_neg
  Usage    : $pp->num_neg()
  Function : Retrieves the number of negative amino acids in a sequence
  Returns  : Returns the number of negative amino acids in a sequence
  Args     : none

=cut



sub num_neg{

	my $self=shift;

	($self->{'negAA'})=$self->{'output'}=~/<B>Total number of negatively charged residues.*?<\/B>\s*(\d*)/;

	return $self->{'negAA'};


}

=head2 num_pos

  Title    : num_pos
  Usage    : $pp->num_pos()
  Function : Retrieves the number of positive amino acids in a sequence
  Returns  : Returns the number of positive amino acids in a sequence
  Args     : none

=cut


sub num_pos{
	my $self=shift;
	($self->{'posAA'})=$self->{'output'}=~/<B>Total number of positively charged residues.*?<\/B>\s*(\d*)/;
	return $self->{'posAA'};
}

=head2 amino_acid_number

  Title    : amino_acid_number
  Usage    : $pp->amino_acid_number()
  Function : Retrieves the number of amino acids within a sequence
  Returns  : Returns the number of amino acids within a sequence
  Args     : none

=cut

sub amino_acid_number{
	my $self=shift;
	($self->{'numAA'})=$self->{'output'}=~/<B>Number of amino acids:<\/B> (\d+)/;