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Bio/Tools/Analysis/DNA/ESEfinder.pm  view on Meta::CPAN

This the second implementation of Bio::SimpleAnalysisI which hopefully
will make it easier to write wrappers on various services. This class
uses a web resource and therefore inherits from L<Bio::WebAgent>.

=head1 SEE ALSO

L<Bio::SimpleAnalysisI>, 
L<Bio::WebAgent>

=head1 FEEDBACK

=head2 Mailing Lists

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists.  Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

=head2 Support 

Please direct usage questions or support issues to the mailing list:

I<bioperl-l@bioperl.org>

rather than to the module maintainer directly. Many experienced and 
reponsive experts will be able look at the problem and quickly 
address it. Please include a thorough description of the problem 
with code and data examples if at all possible.

=head2 Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution.  Bug reports can be submitted via the
web:

  https://github.com/bioperl/bioperl-live/issues

=head1 AUTHORS

Richard Adams, Richard.Adams@ed.ac.uk, 
Heikki Lehvaslaiho, heikki-at-bioperl-dot-org

=head1 APPENDIX

The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _

=cut


# Let the code begin...
#should have own 

package Bio::Tools::Analysis::DNA::ESEfinder;

use Data::Dumper;
use IO::String;
use Bio::SeqIO;
use HTTP::Request::Common qw (POST);
use HTML::HeadParser;
use Bio::SeqFeature::Generic;
use Bio::Seq::Meta::Array;
use Bio::WebAgent;
use strict;

#inherits directly from SimpleAnalysisBase
use base qw(Bio::Tools::Analysis::SimpleAnalysisBase);


#global vars are now file-scoped lexicals

my $URL = 'http://rulai.cshl.org/cgi-bin/tools/ESE/esefinder.cgi';
	
my $ANALYSIS_NAME = 'ESEfinder';


my $ANALYSIS_SPEC =
    {
     'name' => 'ESEfinder',
     'type' => 'DNA', #compulsory entry as is used for seq checking
     'version' => '2.0',
     'supplier' => 'Krainer lab, Cold Spring Harbor Laboratory, POBOX100, Bungtown Rd, COld Spring Harbor, NY, USA',
     'description' => 'to identify exonic splicing elements in human transcripts',
    };

my $INPUT_SPEC =
    [{
      'mandatory' => 'true',
      'type' => 'Bio::PrimarySeqI',
      'name' => 'sequence',
     }];

my $RESULT_SPEC =
    {
     '' => 'bulk',  # same as undef
     'Bio::SeqFeatureI' => 'ARRAY of Bio::SeqFeature::Generic',
     'raw' => 'Array of [ SR_protein, position, motif, score]',
     'all' => 'Bio::Seq::Meta::Array object'
    };


### unique to this module ##
sub _init {
    ## fills in fixed data for class ##
    my $self = shift;
    $self->url($URL);
    $self->{'_ANALYSIS_SPEC'} =$ANALYSIS_SPEC;
    $self->{'_INPUT_SPEC'} =$INPUT_SPEC;
    $self->{'_RESULT_SPEC'} =$RESULT_SPEC;
    $self->{'_ANALYSIS_NAME'} =$ANALYSIS_NAME;
    return $self;
}


sub _run {
    my $self  = shift;
    my $seq_fasta;
    my $stringfh = IO::String->new($seq_fasta);
    my $seqout = Bio::SeqIO->new(-fh => $stringfh,