class Bio::Ensembl
Codes for backward-compatibility.
Constants
- EBIServerURI
- ENSEMBL_URL
Attributes
Organism name. (ex. 'Homo_sapiens').
Server URL (ex. 'www.ensembl.org')
Public Class Methods
# File lib/bio/io/ensembl.rb, line 79 def self.human self.new("Homo_sapiens") end
# File lib/bio/io/ensembl.rb, line 83 def self.mouse self.new("Mus_musculus") end
# File lib/bio/io/ensembl.rb, line 73 def initialize(organism, server = nil) @server = server || ENSEMBL_URL @organism = organism @uri = [ @server.chomp('/'), @organism ].join('/') end
# File lib/bio/io/ensembl.rb, line 204 def self.server_uri(uri = nil) if uri @uri = uri else @uri || EBIServerURI end end
Public Instance Methods
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¶ ↑
#exportview method allow both orderd arguments and named arguments. (Note: mandatory arguments are marked by '*').
Orderd Arguments¶ ↑
-
seq_region_name - Chromosome number (*)
-
anchor1 - From coordination (*)
-
anchor2 - To coordination (*)
-
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']
# File lib/bio/io/ensembl.rb, line 148 def exportview(*args) defaults = { :type1 => 'bp', :type2 => 'bp', :downstream => '', :upstream => '', :format => 'fasta', :options => [], :action => 'export', :_format => 'Text', :output => 'txt', :submit => 'Continue >>' } if args.first.class == Hash options = args.first if options[:options] and options[:format] != 'fasta' and options[:format] != 'tab' options.update({:format => 'gff'}) end else options = { :seq_region_name => args[0], :anchor1 => args[1], :anchor2 => args[2], } case args[3] when Array options.update({:format => 'gff', :options => args[3]}) when Hash options.update(args[3]) end if args[4].class == Hash options.update(args[4]) end end params = defaults.update(options) result = Bio::Command.post_form("#{@uri}/exportview", params) return result.body end