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:[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 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();
specversions : Retrieve a server's DAS specification version for a request URL
my $version = $das->specversions($url); # e.g. 1.53, 1.6, 1.6E my $version_hashref = $das->specversions();
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 callbuild_requests
Constructs the WWW::Curl callbackspostprocess
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.
AUTHOR
Roger Pettett, <[email protected]>LICENSE AND COPYRIGHT
Copyright (C) 2007 GRL, by Roger PettettThis 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.