ktym

#!/usr/bin/env ruby
#
# % gem install linkeddata
# % lodconvert.rb -h
# % lodconvert.rb [-i input_format] [-o output_format] inputfile > outputfile
#

require 'rubygems'
require 'linkeddata'
require 'getoptlong'

ktym

パスウェイデータベースを使ってみる

Pathguide

まずは、様々なパスウェイデータベースの一覧を見てみましょう。

• http://www.pathguide.org/

500 以上のデータベースが下記の分類でリストアップされています。

ktym

#!/usr/bin/env ruby-2.3

=begin
# SPARQL endpoint
https://stirdf.jglobal.jst.go.jp/sparql

# SPARQL query
select *
where {
  ?term a skos:Concept ;

ktym

# Dockerfile for https://github.com/dbcls/sparqlist

FROM ubuntu:16.04

ARG node_version=v7.9.0

RUN apt-get -qq update && apt-get -qq install -y \
    pkg-config \
    sudo \
    curl \

ktym

#!/usr/bin/env ruby                                                                                  

matrix = []

ARGF.each do |line|
  ary = line.strip.split
  matrix << ary
end

matrix.transpose.each do |row|

ktym

#!/usr/bin/env ruby

require 'json'

uniq = File.open("uniq_node.txt").map {|x| x.stip.to_i}

json = JSON.parse(ARGF.read)

json.each do |ary|
  read_id = ary.shift

ktym

@prefix :     <http://rdf.identifiers.org/ontology/> .
@prefix owl:  <http://www.w3.org/2002/07/owl#> .
@prefix rdf:  <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix xsd:  <http://www.w3.org/2001/XMLSchema#> .
@prefix dct:  <http://purl.org/dc/terms/> .
@prefix foaf: <http://xmlns.com/foaf/0.1/> .
@prefix skos: <http://www.w3.org/2004/02/skos/core#> .
@prefix sio:  <http://semanticscience.org/resource/> .
@prefix mirc: <http://identifiers.org/miriam.collection/MIR:> .

ktym

#!/usr/bin/env ruby
#
# https://qiita.com/erukiti/items/f11f448d3f4d73fbc1f9
# https://research.preferred.jp/2012/11/burrows-wheeler-transform-lf-mapping/
#

class BWT

  def initialize(str)
    @str = str + '$'

ktym

#!/usr/bin/env ruby

=begin
# Pairwise sequence alignment algorithms

Currently implements Needleman-Wunsch, Smith-Waterman
and Needleman-Wunsch-Gotoh algorithms based on
the Dynamic Programming (DP).

## Coordinates

ktym

"""
Example RDF/Turtle:

hnt:A0A024QYV7-Q00653
    bp3:dataSource <http://identifiers.org/HINT> ;
    bp3:displayName "A0A024QYV7-Q00653"^^xsd:string ;
    bp3:evidence   pint:evidence-pubmed_14743216-MI_0007-literature-curated , pint:evidence-pubmed_14743216-MI_0676-literature-curated  ;
    bp3:name "A0A024QYV7-Q00653"^^xsd:string ;
    bp3:participant [
        obo:BFO_0000051 uni:A0A024QYV7 ;