Mitsuteru Nakao nakao
nakao
/ a.rb
Created
December 20, 2013 06:52
a bioruby code for http://twitter.com/motthy/status/413701761468084224
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| # Split a multi fasta file into single fasta files (1.fasta, 2.fasta, ...) | |
| # > ruby a.rb multi.fasta | |
| require 'rubygems' | |
| gem 'bio' | |
| Bio::FlatFile.auto($<).each_with_index do |entry, i| | |
| File.open("#{i+1}.fasta", "w") do |f| | |
| f.puts entry.to_s | |
| end |
nakao
/ gist:5966847
Last active
December 19, 2015 14:09
Fix invalid ChEMBL-RDF files. Put the script in the ChEMBL-RDF directory, then exec. You get fixed files as "*.ttl.new"
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| files = ["chembl_16_biocmpt.ttl", "chembl_16_target.ttl", "chembl_16_targetcmpt.ttl"] | |
| def iotax(arg) | |
| "<http://identifiers.org/taxonomy/#{arg}>" | |
| end | |
| def ncbitax(arg) | |
| "<http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=#{arg}>" | |
| end |
nakao
/ gist:5882712
Last active
December 19, 2015 02:28
List human proteins (protein id, gene label, disease mnemonic, disease id and omim id) which have disease annotation. UniProt SPARQL endpoint http://beta.sparql.uniprot.org/
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| PREFIX rdf:<http://www.w3.org/1999/02/22-rdf-syntax-ns#> | |
| PREFIX skos:<http://www.w3.org/2004/02/skos/core#> | |
| PREFIX owl:<http://www.w3.org/2002/07/owl#> | |
| PREFIX bibo:<http://purl.org/ontology/bibo/> | |
| PREFIX dc:<http://purl.org/dc/terms/> | |
| PREFIX xsd:<http://www.w3.org/2001/XMLSchema#> | |
| PREFIX up:<http://purl.uniprot.org/core/> | |
| PREFIX rdfs:<http://www.w3.org/2000/01/rdf-schema#> | |
| Select ?protein ?geneLabel ?dMnemonic ?disease ?omim |
nakao
/ gist:5881623
Last active
December 19, 2015 02:18
List human proteins which have natural variants described also in OMIM. The query returns protein id, gene label, mutation(cf. A301R), omim id and citation id at UniProt SPARQL endpoint http://beta.sparql.uniprot.org/sparql .
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| PREFIX rdf:<http://www.w3.org/1999/02/22-rdf-syntax-ns#> | |
| PREFIX skos:<http://www.w3.org/2004/02/skos/core#> | |
| PREFIX owl:<http://www.w3.org/2002/07/owl#> | |
| PREFIX bibo:<http://purl.org/ontology/bibo/> | |
| PREFIX dc:<http://purl.org/dc/terms/> | |
| PREFIX xsd:<http://www.w3.org/2001/XMLSchema#> | |
| PREFIX up:<http://purl.uniprot.org/core/> | |
| PREFIX rdfs:<http://www.w3.org/2000/01/rdf-schema#> | |
| SELECT ?protein ?geneLabel ?hgsv ?omim ?citation |
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| require 'rubygems' | |
| require 'rdf' | |
| require 'rest_client' | |
| require 'json' | |
| task "probeset.js" do | |
| endpoint = "http://open-biomed.org:8890/sparql" | |
| query = "SELECT * WHERE { GRAPH <http://open-biomed.org:8890/DAV/BH11Ujicha/HG-U133A.na31.annot> { ?subject ?predicate ?object } }" |
nakao
/ sample-sparql.rb
Created
August 25, 2011 08:01
Sample Ruby code for the BH11Ujicha SPARQL endpoint
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| require 'rubygems' | |
| require 'rdf' # gem install rdf | |
| require 'rest_client' # gem install rest-client | |
| require 'json' # gem install json | |
| endpoint = "http://open-biomed.org:8890/sparql" | |
| query = "SELECT * WHERE { <http://bio2rdf.org/affymetrix:1007_s_at> ?predicate ?object }" | |
| # XML, "application/sparql-results+xml" ; CSV, "text/csv" | |
| response = RestClient.post endpoint, :query => query, :format => "application/sparql-results+json" |
nakao
/ usegalaxy-tweets.rb
Created
May 27, 2011 11:08
Extracting tweets from 2011 Galaxy Community Conference #usegalaxy
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| # https://twitter.com/#!/pjacock/status/74029124242505728 | |
| # https://twitter.com/#!/32nm/status/74070121219497984 | |
| require 'rubygems' | |
| require 'open-uri' | |
| require 'nokogiri' | |
| url = "http://togetter.com/li/140056" | |
| doc = Nokogiri::HTML(open(url).read) | |
| puts doc.xpath("//div[@class='status']/a").map {|x| x.attribute("href").value } |
nakao
/ gist:641871
Created
October 23, 2010 06:29
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| require 'bio' | |
| class Bio::Sequence::NA | |
| def self.compute_melting_temperature(nastr) | |
| 10 # code here ... | |
| end | |
| def melting_temperature | |
| if @melting_temperature | |
| @melting_temperature |
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| # ruby tkana.rb http://twitter.com/synobu/status/20976018979 | |
| require 'rubygems' | |
| require 'nokogiri' | |
| require 'open-uri' | |
| require 'htmlentities' | |
| url = ARGV[0] | |
| doc = Nokogiri::XML.parse(open(url).read) | |
| t = (doc/"span.entry-content").to_s.gsub(/<.+?>/,'') |