An Ensembl Genome Browser client class.
human = Bio::Ensembl.new('Homo_sapiens') seq = human.exportview(1, 1000, 100000) gff = human.exportview(1, 1000, 100000, ['gene']) mouse = Bio::Ensembl.new('Mus_musculus') seq = mouse.exportview(1, 1000, 100000) gff = mouse.exportview(1, 1000, 100000, ['gene', 'variation', 'genscan']) rice = Bio::Enesmbl.new('Oryza_sativa', 'http://www.gramene.org') seq = rice.exportview(1, 1000, 100000)
GRAMENE www.gramene.org/
Codes for backward-compatibility.
# 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
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).
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')
Bio::Ensembl#exportview method allow both orderd arguments and named arguments. (Note: mandatory arguments are marked by '*').
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']
: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
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