[Source]

    # File lib/bio/io/ensembl.rb, line 79
79:   def self.human
80:     self.new("Homo_sapiens")
81:   end

[Source]

    # File lib/bio/io/ensembl.rb, line 83
83:   def self.mouse
84:     self.new("Mus_musculus")
85:   end

[Source]

    # File lib/bio/io/ensembl.rb, line 73
73:   def initialize(organism, server = nil)
74:     @server = server || ENSEMBL_URL
75:     @organism = organism
76:     @uri = [ @server.chomp('/'), @organism ].join('/')
77:   end

[Source]

     # File lib/bio/io/ensembl.rb, line 204
204:   def self.server_uri(uri = nil)
205:     if uri
206:       @uri = uri
207:     else
208:       @uri || EBIServerURI
209:     end
210:   end

Ensembl ExportView Client.

Retrieve genomic sequence/features from Ensembl ExportView in plain text. Ensembl ExportView exports genomic data (sequence and features) in several file formats including fasta, GFF and tab.

• ExportViwe (www.ensembl.org/Homo_sapiens/exportview).

Examples

  human = Bio::Ensembl.new('Homo_sapiens')
    or
  human = Bio::Ensembl.human

  # Genomic sequence in Fasta format
  human.exportview(:seq_region_name => 1,
                   :anchor1 => 1149206, :anchor2 => 1149229)
  human.exportview(1, 1149206, 1149229)

  # Feature in GFF
  human.exportview(:seq_region_name => 1,
                   :anchor1 => 1149206, :anchor2 => 1150000,
                   :options => ['similarity', 'repeat',
                                'genscan', 'variation', 'gene'])
  human.exportview(1, 1149206, 1150000, ['variation', 'gene'])

Feature in TAB

  human.exportview(:seq_region_name => 1,
                   :anchor1 => 1149206, :anchor2 => 1150000,
                   :options => ['similarity', 'repeat',
                                'genscan', 'variation', 'gene'],
                   :format => 'tab')

Arguments

Bio::Ensembl#exportview method allow both orderd arguments and named arguments. (Note: mandatory arguments are marked by ’*’).

Orderd Arguments

1. seq_region_name - Chromosome number (*)
2. anchor1 - From coordination (*)
3. anchor2 - To coordination (*)
4. options - Features to export (in :format => ‘gff’ or ‘tab’)

                     ['similarity', 'repeat', 'genscan', 'variation',
                      'gene']
   

Named Arguments

• :seq_region_name - Chromosome number (*)
• :anchor1 - From coordination (*)
• :anchor2 - To coordination (*)
• :type1 - From coordination type [‘bp’, ]
• :type2 - To coordination type [‘bp’, ]
• :upstream - Bp upstream
• :downstream - Bp downstream
• :format - File format [‘fasta’, ‘gff’, ‘tab’]
• :options - Features to export (for :format => ‘gff’ or ‘tab’)

                     ['similarity', 'repeat', 'genscan', 'variation',
                      'gene']
  

[Source]

     # File lib/bio/io/ensembl.rb, line 148
148:   def exportview(*args)
149:     defaults = {
150:       :type1 => 'bp', 
151:       :type2 => 'bp', 
152:       :downstream => '', 
153:       :upstream => '', 
154:       :format => 'fasta',
155:       :options => [],
156:       :action => 'export', 
157:       :_format => 'Text', 
158:       :output => 'txt', 
159:       :submit => 'Continue >>'
160:     }
161: 
162:     if args.first.class == Hash
163:       options = args.first
164:       if options[:options] and options[:format] != 'fasta' and options[:format] != 'tab' 
165:         options.update({:format => 'gff'}) 
166:       end
167:     else
168:       options = {
169:         :seq_region_name => args[0], 
170:         :anchor1 => args[1], 
171:         :anchor2 => args[2],
172:       }
173: 
174:       case args[3]
175:       when Array
176:         options.update({:format => 'gff', :options => args[3]}) 
177:       when Hash
178:         options.update(args[3])
179:       end
180: 
181:       if args[4].class == Hash
182:         options.update(args[4])
183:       end
184:     end
185: 
186:     params = defaults.update(options)
187: 
188:     result = Bio::Command.post_form("#{@uri}/exportview", params)
189: 
190:     return result.body
191:   end