NAME

Bio::DasLite - Perl extension for the DAS (HTTP+XML) Protocol (http://biodas.org/)

SYNOPSIS

  use Bio::DasLite;

  my $das = Bio::DasLite->new({
                               'timeout'    => 60,                                       # optional timeout in seconds
                               'dsn'        => "http://das.ensembl.org/das/ensembl1834", # optional DSN (scalar, or arrayref)
                               'http_proxy' => "http://webcache.local.com:3128",         # optional http proxy
                              });

  $das->dsn("http://das.ensembl.org/das/ensembl1834/"); # give dsn (scalar or arrayref) here if not specified in new()

  #########
  # Retrieve other sources from the same service
  #
  my $src_data      = $das->dsns();

  #########
  # Retrieve entry_points, e.g. chromosomes and associated information (e.g. sequence length and version)
  #
  my $entry_points  = $das->entry_points();

  #########
  # Retrieve sequence data (probably dna or protein)
  #
  my $sequence      = $das->sequence("2:1,1000"); # segment:start,stop (e.g. chromosome 2, bases 1 to 1000)

  #########
  # Find out about different data types available from this source
  #
  my $types         = $das->types(); # takes optional args - see DAS specs

  #########
  # Different ways to fetch features -
  #
  my $feature_data1 = $das->features("1:1,100000");
  my $feature_data2 = $das->features(["1:1,100000", "2:20435000,21435000"]);
  my $feature_data3 = $das->features({
                                      'segment' => "1:1,1000",
                                      'type'    => "karyotype",
                                      # optional args - see DAS Spec
                                     });
  my $feature_data4 = $das->features([
                                      {'segment' => "1:1,1000000",'type' => 'karyotype',},
                                      {'segment' => "2:1,1000000",},
                                     ]);

  #########
  # Feature fetch with callback
  #
  my $callback = sub {
                my $struct = shift;
                print STDERR Dumper($struct);
               };
  # then:
  $das->callback($callback);
  $das->features("1:1,1000000");

  # or:
  $das->features("1:1,1000000", $callback);

  # or:
  $das->features(["1:1,1000000", "2:1,1000000", "3:1,1000000"], $callback);

  #########
  # Fetch a stylesheet structure
  #
  my $style_data    = $das->stylesheet();

  my $style_data2   = $das->stylesheet($callback);

DESCRIPTION

This module is an implementation of a client for the DAS protocol (XML over HTTP primarily for biological-data). It requires LWP::Parallel::UserAgent.

SEE ALSO

DAS Specifications at: http://biodas.org/documents/spec.html

ProServer (A DAS Server implementation) at: http://www.sanger.ac.uk/proserver/

The venerable Bio::Das suite (CPAN and http://www.biodas.org/download/Bio::Das/).

KNOWN BUGS

On certain platforms the 'stylesheet' request segfaults complaining about free()ing an invalid pointer. e.g. it works find on my Mac, but not on Linux or Alpha (various perl versions).

AUTHOR

Roger Pettett, <rmp@sanger.ac.uk>

COPYRIGHT AND LICENSE

Copyright (C) 2005 by Roger Pettett

This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself, either Perl version 5.8.4 or, at your option, any later version of Perl 5 you may have available.