Bio::Das::Lite(3pm)					User Contributed Perl Documentation				       Bio::Das::Lite(3pm)

NAME

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

VERSION

	 See $Bio::Das::Lite::VERSION

SYNOPSIS

	 use Bio::Das::Lite;
	 my $bdl     = Bio::Das::Lite->new_from_registry({'category' => 'GRCh_37,Chromosome,Homo sapiens'});
	 my $results = $bdl->features('22');

SUBROUTINES
/METHODS
   new : Constructor
	 my $das = Bio::Das::Lite->new('http://das.ensembl.org/das/ensembl1834');

	 my $das = Bio::Das::Lite->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)
			no_proxy   (optional list/ref, non-proxiable domains 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 'capability' and 'category'
	 in the given hashref, using them to query the DAS registry and
	 configuring the DSNs accordingly.

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

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

	 For a complete list of capabilities and categories, see:

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

	 The category can optionally be a full coordinate system name,
	 allowing further restriction by authority, version and species.
	 For example:
	     'Protein Sequence' OR
	     'UniProt,Protein Sequence' OR
	     'GRCh_37,Chromosome,Homo sapiens'

   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');

   no_proxy : Get/Set domains to not use proxy for
	   $das->no_proxy('ebi.ac.uk', 'localhost');
	   OR
	   $das->no_proxy( ['ebi.ac.uk', 'localhost'] );

	   Always returns an arrayref

   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',},
					     {'group_id' => 'OTTHUMG00000036084',},
					    ]);

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

	 # or:
	 $das->features([{'group_id' => 'OTTHUMG00000036084'}, '2:1,1000000', '3:1,1000000'], $callback);

   alignment : Retrieve protein alignment data for a query.  This can be a multiple sequence alignment or pairwise alignment.  Note - this has not
       been tested for structural alignments as there is currently no Das source avialable.
	 my $alignment = $das->alignment({query => 'Q01234'});

   structure : Retrieve known structure (i.e. PDB) for a query
	 my $structure = $das->structure({ query => 'pdb_id'});

   sources : Retrieves the list of sources form the DAS registry, via a DAS call.
	 my $sources = $das->source;

   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_hosts set number of running concurrent host connections
	 THIS METHOD IS NOW DEPRECATED AND HAS NO EFFECT

	 $das->max_hosts(7);
	 print $das->max_hosts();

   max_req set number of running concurrent requests per host
	 THIS METHOD IS NOW DEPRECATED AND HAS NO EFFECT

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

   registry : Get/Set accessor for DAS-Registry service URLs
	 $biodaslite->registry('http://www.dasregistry.org/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'],
	 });

   build_queries
       Constructs an arrayref of DAS requests including parameters for each call

   build_requests
       Constructs the WWW::Curl callbacks

   postprocess
       Applies processing to the result set, e.g. removal of whitespace from sequence responses.

DESCRIPTION

       This module is an implementation of a client for the DAS protocol (XML over HTTP primarily for biological-data).

DEPENDENCIES

       strict
       warnings
       WWW::Curl
       HTTP::Response
       Carp
       English
       Readonly

DIAGNOSTICS

	 Set $Bio::Das::Lite::DEBUG = 1;

CONFIGURATION AND ENVIRONMENT

INCOMPATIBILITIES

BUGS AND LIMITATIONS

	 The max_req and max_hosts methods are now deprecated and have no effect.

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, <rpettett@cpan.org>

LICENSE AND COPYRIGHT

       Copyright (C) 2007 GRL, 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.

perl v5.14.2							    2011-11-26						       Bio::Das::Lite(3pm)