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/Sethttp_proxy
$das->http_proxy('http://user:pass@squid.myco.com:3128/');
proxy_user:Get/Setproxyusernameforauthenticatingforward-proxies
This is only required if the username wasn't specified when setting http_proxy
$das->proxy_user('myusername');
proxy_pass:Get/Setproxypasswordforauthenticatingforward-proxies
This is only required if the password wasn't specified when setting http_proxy
$das->proxy_pass('secretpassword');
no_proxy:Get/Setdomainstonotuseproxyfor
$das->no_proxy('ebi.ac.uk', 'localhost');
OR
$das->no_proxy( ['ebi.ac.uk', 'localhost'] );
Always returns an arrayref
user_agent:Get/Setuser-agentforrequestheaders
$das->user_agent('GroovyDAS/1.0');
timeout:Get/Settimeout
$das->timeout(30);
caching:Get/Setcaching
$das->caching(1);
callback:Get/Setcallbackcoderef
$das->callback(sub { });
basename:GetbaseURL(s)ofservice
$das->basename(optional $dsn);
dsn:Get/SetDSN
$das->dsn('http://das.ensembl.org/das/ensembl1834/'); # give dsn (scalar or arrayref) here if not specified in new()
Or, if you want to add to the existing dsn list and you're feeling sneaky...
push @{$das->dsn}, 'http://my.server/das/additionalsource';
dsns:Retrieveinformationaboutothersourcesservedfromthisserver.
Note this call is 'dsns', as differentiated from 'dsn' which is the current configured source
my $src_data = $das->dsns();
entry_points:Retrievethelistofentry_pointsforthissource
e.g. chromosomes and associated information (e.g. sequence length and version)
my $entry_points = $das->entry_points();
Typesofargumentfor'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:Findoutaboutdifferentdatatypesavailablefromthissource
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:Retrievefeaturesfromasegment
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:Retrieveproteinalignmentdataforaquery.Thiscanbeamultiplesequencealignmentorpairwisealignment.Note-thishasnotbeentestedforstructuralalignmentsasthereiscurrentlynoDassourceavialable.
my $alignment = $das->alignment({query => 'Q01234'});
structure:Retrieveknownstructure(i.e.PDB)foraquery
my $structure = $das->structure({ query => 'pdb_id'});
sources:RetrievesthelistofsourcesformtheDASregistry,viaaDAScall.
my $sources = $das->source;
sequence:Retrievesequencedataforasegment(probablydnaorprotein)
my $sequence = $das->sequence('2:1,1000'); # segment:start,stop (e.g. chromosome 2, bases 1 to 1000)
stylesheet:Retrievestylesheetdata
my $style_data = $das->stylesheet();
my $style_data2 = $das->stylesheet($callback);
statuscodes:RetrieveHTTPstatuscodesforrequestURLs
my $code = $das->statuscodes($url);
my $code_hashref = $das->statuscodes();
specversions:Retrieveaserver'sDASspecificationversionforarequestURL
my $version = $das->specversions($url); # e.g. 1.53, 1.6, 1.6E
my $version_hashref = $das->specversions();
max_hostssetnumberofrunningconcurrenthostconnections
THIS METHOD IS NOW DEPRECATED AND HAS NO EFFECT
$das->max_hosts(7);
print $das->max_hosts();
max_reqsetnumberofrunningconcurrentrequestsperhost
THIS METHOD IS NOW DEPRECATED AND HAS NO EFFECT
$das->max_req(5);
print $das->max_req();
registry:Get/SetaccessorforDAS-RegistryserviceURLs
$biodaslite->registry('http://www.dasregistry.org/das');
my $registry_arrayref = $biodaslite->registry();
registry_sources:Arrayrefofdassourceobjectsfromtheconfiguredregistryservices
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.
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