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 / 
Bio-DasLite-1.38
/ Bio::DasLite

NAME

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

SYNOPSIS

  use Bio::DasLite;
  my $bdl     = Bio::DasLite->new_from_registry({'category' => 'Chromosome'});
  my $results = $bdl->features("22");

METHODS

new : Constructor

  my $das = Bio::DasLite->new("http://das.ensembl.org/das/ensembl1834");

  my $das = Bio::DasLite->new({
                               'timeout'    => 60,
                               'dsn'        => 'http://user:pass@das.ensembl.org/das/ensembl1834',
                               'http_proxy' => 'http://user:pass@webcache.local.com:3128/',
                              });

 Options can be: dsn        (optional scalar or array ref, URLs of DAS services)
                 timeout    (optional int,      HTTP fetch timeout in seconds)
                 http_proxy (optional scalar,   web cache or proxy if not set in %ENV)
                 caching    (optional bool,     primitive caching on/off)
                 callback   (optional code ref, callback for processed XML blocks)
                 registry   (optional array ref containing DAS registry service URLs
                             defaults to 'http://das.sanger.ac.uk/registry/services/das')
                 proxy_user (optional scalar,   username for authenticating forward-proxy)
                 proxy_pass (optional scalar,   password for authenticating forward-proxy)
                 user_agent (optional scalar,   User-Agent HTTP request header value)

new_from_registry : Constructor

  Similar to 'new' above but supports 'capabilities' and 'category'
  in the given hashref, using them to query the DAS registry and
  configuring the DSNs accordingly.

  my $das = Bio::DasLite->new_from_registry({
                                             'capabilities' => ['features'],
                                             'category'     => ['Protein Sequence'],
                                            });

 Options are as above, plus
                 capability   (optional arrayref of capabilities)
                 category     (optional arrayref of categories)

For a complete list of capabilities and categories, see:

    http://das.sanger.ac.uk/registry/

http_proxy : Get/Set http_proxy

    $das->http_proxy("http://user:pass@squid.myco.com:3128/");

proxy_user : Get/Set proxy username for authenticating forward-proxies

  This is only required if the username wasn't specified when setting http_proxy

    $das->proxy_user("myusername");

proxy_pass : Get/Set proxy password for authenticating forward-proxies

  This is only required if the password wasn't specified when setting http_proxy

    $das->proxy_pass("secretpassword");

user_agent : Get/Set user-agent for request headers

    $das->user_agent("GroovyDAS/1.0");

timeout : Get/Set timeout

    $das->timeout(30);

caching : Get/Set caching

    $das->caching(1);

callback : Get/Set callback code ref

    $das->callback(sub { });

basename : Get base URL(s) of service

    $das->basename(optional $dsn);

dsn : Get/Set DSN

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

  Or, if you want to add to the existing dsn list and you're feeling sneaky...

  push @{$das->dsn}, "http://my.server/das/additionalsource";

dsns : Retrieve information about other sources served from this server.

 Note this call is 'dsns', as differentiated from 'dsn' which is the current configured source

  my $src_data = $das->dsns();

entry_points : Retrieve the list of entry_points for this source

  e.g. chromosomes and associated information (e.g. sequence length and version)

  my $entry_points  = $das->entry_points();

Types of argument for 'types', 'features', 'sequence' calls:

  Segment Id:
  "1"

  Segment Id with range:
  "1:1,1000"

  Segment Id with range and type:
  {
    'segment' => "1:1,1000",
    'type'    => 'exon',
  }

  Multiple Ids with ranges and types:
  [
    {
      'segment' => "1:1,1000",
      'type'    => 'exon',
    },
    {
      'segment' => "2:1,1000",
      'type'    => 'exon',
    },
  ]

  See DAS specifications for other parameters

types : Find out about different data types available from this source

  my $types         = $das->types(); # takes optional args - see DAS specs

 Retrieve the types of data available for this source
 e.g. 32k_cloneset, karyotype, swissprot

features : Retrieve features from a segment

   e.g. clones on a chromosome

  #########
  # 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);

sequence : Retrieve sequence data for a segment (probably dna or protein)

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

stylesheet : Retrieve stylesheet data

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

statuscodes : Retrieve HTTP status codes for request URLs

  my $code         = $das->statuscodes($url);
  my $code_hashref = $das->statuscodes();

max_req set number of running concurrent requests

  $das->max_req(5);
  print $das->max_req();

registry : Get/Set accessor for DAS-Registry service URLs

  $biodaslite->registry('http://das.sanger.ac.uk/registry/das');

  my $registry_arrayref = $biodaslite->registry();

registry_sources : Arrayref of dassource objects from the configured registry services

  my $sources_ref = $biodaslite->registry_sources();

  my $sources_ref = $biodaslite->registry_sources({
    'capability' => ['features','stylesheet'],
  });

  my $sources_ref = $biodaslite->registry_sources({
    'category' => ['Protein Sequence'],
  });

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 also by the author) at: http://www.sanger.ac.uk/proserver/

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

The DAS Registry at: http://das.sanger.ac.uk/registry/

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.