togostanza 2.0.0 → 2.1.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +4 -4
- data/lib/togostanza/cli.rb +1 -0
- data/lib/togostanza/stanza/querying.rb +11 -25
- data/lib/togostanza/version.rb +1 -1
- metadata +2 -2
checksums.yaml
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@@ -1,7 +1,7 @@
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---
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SHA1:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 0379c6310562da1453a679c51d90c6496ae83095
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data.tar.gz: 1073dd02b8261acf5780349581f07243523d2182
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SHA512:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 0d4292ab3bff30defb01f8fbe94aaf37c3f2d9a1e9388d21b4188df4ed11d171baec65efa474e14c97c6738c590b9b06ddc7fc84ac2f82bbb73a5dc697955c6c
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data.tar.gz: a7839f24738a41d013e1650bbd9e3704dd08baa8b41e64c8016e32813100e99dfcc8cb90adf1d20d17adda90ec15ed8bc3739361c7601d83e04ae26aa15c733f
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data/lib/togostanza/cli.rb
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@@ -1,43 +1,29 @@
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require 'sparql/client'
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require 'flavour_saver'
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module TogoStanza::Stanza
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module Querying
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MAPPINGS = {
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togogenome: 'http://
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uniprot: 'http://ep.dbcls.jp/sparql7',
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go: 'http://ep.dbcls.jp/sparql7'
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togogenome: 'http://togogenome.org/sparql'
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}
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def query(endpoint,
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def query(endpoint, text_or_filename)
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path = File.join(root, 'sparql', text_or_filename)
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if File.exist?(path)
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data = OpenStruct.new params
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text_or_filename = Tilt.new(path).render(data)
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end
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client = SPARQL::Client.new(MAPPINGS[endpoint] || endpoint)
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#Rails.logger.debug "SPARQL QUERY: \n#{sparql}"
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client.query(
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client.query(text_or_filename).map {|binding|
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binding.each_with_object({}) {|(name, term), hash|
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hash[name] = term.to_s
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}
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}
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end
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def uniprot_url_from_togogenome(gene_id)
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# refseq の UniProt
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# slr1311 の時 "http://purl.uniprot.org/refseq/NP_439906.1"
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query(:togogenome, <<-SPARQL).first[:up]
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PREFIX insdc: <http://insdc.org/owl/>
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PREFIX idorg: <http://rdf.identifiers.org/database/>
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SELECT DISTINCT ?up
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FROM <http://togogenome.org/graph/refseq/>
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WHERE {
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?s insdc:feature_locus_tag "#{gene_id}" .
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?s rdfs:seeAlso ?np .
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?s rdfs:seeAlso ?xref .
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?np rdf:type idorg:Protein .
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BIND (STRAFTER(STR(?np), "ncbiprotein/") AS ?npid)
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BIND (IRI(CONCAT("http://purl.uniprot.org/refseq/", ?npid)) AS ?up)
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}
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SPARQL
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end
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end
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end
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data/lib/togostanza/version.rb
CHANGED
metadata
CHANGED
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@@ -1,14 +1,14 @@
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--- !ruby/object:Gem::Specification
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name: togostanza
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version: !ruby/object:Gem::Version
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version: 2.
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version: 2.1.0
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platform: ruby
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authors:
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- Keita Urashima
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autorequire:
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bindir: bin
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cert_chain: []
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date: 2015-11-
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date: 2015-11-25 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: activesupport
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