Bio::Das::Lite: Perl extension for the das (http+xml) protocol (http://biodas.org/)

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:[email protected]/das/ensembl1834', 'http_proxy' => 'http://user:[email protected]: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:[email protected]: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 \s-1URL\s0(s) of service

$das->basename(optional $dsn);

dsn : Get/Set \s-1DSN\s0

$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. \s-1PDB\s0) for a query

my $structure = $das->structure({ query => 'pdb_id'});

sources : Retrieves the list of sources form the \s-1DAS\s0 registry, via a \s-1DAS\s0 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 \s-1HTTP\s0 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 \s-1DAS\s0 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.

Bio::Das::Lite (3pm)

VERSION

SYNOPSIS