class Bio::TogoWS::REST
Description¶ ↑
Bio::TogoWS::REST is a REST client for the TogoWS web service.
Details of the service are desribed in the following URI.
Examples¶ ↑
For light users, class methods can be used.
print Bio::TogoWS::REST.entry('ncbi-nucleotide', 'AF237819') print Bio::TogoWS::REST.search('uniprot', 'lung cancer')
For heavy users, an instance of the REST class can be created, and using the instance is more efficient than using class methods.
t = Bio::TogoWS::REST.new print t.entry('ncbi-nucleotide', 'AF237819') print t.search('uniprot', 'lung cancer')
References¶ ↑
Constants
Attributes
If true, shows debug information to $stderr.
Public Class Methods
Source
# File lib/bio/io/togows.rb 345 def self.convert(*arg) 346 self.new.convert(*arg) 347 end
The same as Bio::TogoWS::REST#convert.
Source
# File lib/bio/io/togows.rb 335 def self.entry(*arg) 336 self.new.entry(*arg) 337 end
The same as Bio::TogoWS::REST#entry.
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# File lib/bio/io/togows.rb 355 def self.entry_database_list(*arg) 356 self.new.entry_database_list(*arg) 357 end
The same as Bio::TogoWS::REST#entry_database_list
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# File lib/bio/io/togows.rb 141 def initialize(uri = BASE_URI) 142 uri = URI.parse(uri) unless uri.kind_of?(URI) 143 @pathbase = uri.path 144 @pathbase = '/' + @pathbase unless /\A\// =~ @pathbase 145 @pathbase = @pathbase + '/' unless /\/\z/ =~ @pathbase 146 @http = Bio::Command.new_http(uri.host, uri.port) 147 @header = { 148 'User-Agent' => "BioRuby/#{Bio::BIORUBY_VERSION_ID}" 149 } 150 @debug = false 151 end
Creates a new object.
Arguments:
-
(optional) uri: String or URI object
- Returns
-
new object
Source
# File lib/bio/io/togows.rb 350 def self.retrieve(*arg) 351 self.new.retrieve(*arg) 352 end
The same as Bio::TogoWS::REST#retrieve.
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# File lib/bio/io/togows.rb 340 def self.search(*arg) 341 self.new.search(*arg) 342 end
The same as Bio::TogoWS::REST#search.
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# File lib/bio/io/togows.rb 360 def self.search_database_list(*arg) 361 self.new.search_database_list(*arg) 362 end
The same as Bio::TogoWS::REST#search_database_list
Public Instance Methods
Source
# File lib/bio/io/togows.rb 310 def convert(data, inputformat, format) 311 response = post_data(data, 'convert', "#{inputformat}.#{format}") 312 313 prepare_return_value(response) 314 end
Data format conversion.
Example:
t = Bio::TogoWS::REST.new blast_string = File.read('test.blastn') t.convert(blast_string, 'blast', 'gff')
Arguments:
-
(required) text: (String) input data
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(required) inputformat: (String) data source format
-
(required) format: (String) output format
- Returns
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String or nil
Source
# File lib/bio/io/togows.rb 241 def entry(database, ids, format = nil, field = nil) 242 begin 243 a = ids.to_ary 244 rescue NoMethodError 245 ids = ids.to_s 246 end 247 248 arg = [ 'entry', database ] 249 if a then 250 b = a.dup 251 (a.size - 1).downto(1) { |i| b.insert(i, :",") } 252 arg.concat b 253 else 254 arg.push ids 255 end 256 257 arg.push field if field 258 arg[-1] = "#{arg[-1]}.#{format}" if format 259 response = get(*arg) 260 261 prepare_return_value(response) 262 end
Retrieves entries corresponding to the specified IDs.
Example:
t = Bio::TogoWS::REST.new kuma = t.entry('ncbi-nucleotide', 'AF237819') # multiple IDs at a time misc = t.entry('ncbi-nucleotide', [ 'AF237819', 'AF237820' ]) # with format change p53 = t.entry('uniprot', 'P53_HUMAN', 'fasta')
Arguments:
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(required) database: (String) database name
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(required) ids: (String) an entry ID, or (Array containing String) IDs. Note that strings containing “,” are regarded as multiple IDs.
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(optional) format: (String) format. nil means the default format (differs depending on the database).
-
(optional) field: (String) gets only the specified field if not nil
- Returns
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String or nil
Source
# File lib/bio/io/togows.rb 319 def entry_database_list 320 database_list('entry') 321 end
Returns list of available databases in the entry service.
- Returns
-
Array containing String
Source
# File lib/bio/io/togows.rb 160 def internal_http 161 @http 162 end
Debug purpose only. Returns Net::HTTP object used inside the object. The method will be changed in the future if the implementation of this class is changed.
Source
# File lib/bio/io/togows.rb 186 def retrieve(ids, hash = {}) 187 begin 188 a = ids.to_ary 189 rescue NoMethodError 190 ids = ids.to_s 191 end 192 ids = a.join(',') if a 193 ids = ids.split(',') 194 195 dbs = hash[:database] || DEFAULT_RETRIEVAL_DATABASES 196 begin 197 dbs.to_ary 198 rescue NoMethodError 199 dbs = dbs.to_s.empty? ? [] : [ dbs.to_s ] 200 end 201 return nil if dbs.empty? or ids.empty? 202 203 if dbs.size == 1 then 204 return entry(dbs[0], ids, hash[:format], hash[:field]) 205 end 206 207 results = [] 208 ids.each do |idstr| 209 dbs.each do |dbstr| 210 r = entry(dbstr, idstr, hash[:format], hash[:field]) 211 if r and !r.strip.empty? then 212 results.push r 213 break 214 end 215 end #dbs.each 216 end #ids.each 217 218 results.join('') 219 end
Intelligent version of the entry method. If two or more databases are specified, sequentially tries them until valid entry is obtained.
If database is not specified, preset default databases are used. See DEFAULT_RETRIEVAL_DATABASES for details.
When multiple IDs and multiple databases are specified, sequentially tries each IDs. Note that results with no hits found or with server errors are regarded as void strings. Also note that data format of the result entries can be different from entries to entries.
Arguments:
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(required) ids: (String) an entry ID, or (Array containing String) IDs. Note that strings containing “,”
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(optional) hash: (Hash) options below can be passed as a hash.
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(optional) :database: (String) database name, or (Array containing String) database names.
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(optional) :format: (String) format
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(optional) :field: (String) gets only the specified field
-
- Returns
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String or nil
Source
# File lib/bio/io/togows.rb 285 def search(database, query, offset = nil, limit = nil, format = nil) 286 arg = [ 'search', database, query ] 287 if offset then 288 limit ||= 1 289 arg.concat [ "#{offset}", :",", "#{limit}" ] 290 end 291 arg[-1] = "#{arg[-1]}.#{format}" if format 292 response = get(*arg) 293 294 prepare_return_value(response) 295 end
Database search. Format of the search term string follows the Common Query Language.
Example:
t = Bio::TogoWS::REST.new print t.search('uniprot', 'lung cancer') # only get the 10th and 11th hit ID print t.search('uniprot', 'lung cancer', 10, 2) # with json format print t.search('uniprot', 'lung cancer', 10, 2, 'json')
Arguments:
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(required) database: (String) database name
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(required) query: (String) query string
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(optional) offset: (Integer) offset in search results.
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(optional) limit: (Integer) max. number of returned results. If offset is not nil and the limit is nil, it is set to 1.
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(optional) format: (String) format. nil means the default format.
- Returns
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String or nil
Source
# File lib/bio/io/togows.rb 326 def search_database_list 327 database_list('search') 328 end
Returns list of available databases in the search service.
- Returns
-
Array containing String