Query: bio::das::lite
OS: debian
Section: 3pm
Format: Original Unix Latex Style Formatted with HTML and a Horizontal Scroll Bar
Bio::Das::Lite(3pm) User Contributed Perl Documentation Bio::Das::Lite(3pm)NAMEBio::Das::Lite - Perl extension for the DAS (HTTP+XML) Protocol (http://biodas.org/)VERSIONSee $Bio::Das::Lite::VERSIONSYNOPSISuse 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.DESCRIPTIONThis module is an implementation of a client for the DAS protocol (XML over HTTP primarily for biological-data).DEPENDENCIESstrict warnings WWW::Curl HTTP::Response Carp English ReadonlyDIAGNOSTICSSet $Bio::Das::Lite::DEBUG = 1;CONFIGURATION AND ENVIRONMENTINCOMPATIBILITIESBUGS AND LIMITATIONSThe max_req and max_hosts methods are now deprecated and have no effect.SEE ALSODAS 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/AUTHORRoger Pettett, <rpettett@cpan.org>LICENSE AND COPYRIGHTCopyright (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)