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Toshiaki Katayama ktym

  • Database Center for Life Science
  • Japan
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@ktym
ktym / dp.rb
Last active Jul 11, 2019
See https://github.com/ktym/dp for newer version.
View dp.rb
#!/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
View bwt.rb
#!/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 + '$'
View idorg-ontology-dblink.owl
View select_reads_on_uniq_path.rb
#!/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
View select_uniq_path.rb
#!/usr/bin/env ruby
matrix = []
ARGF.each do |line|
ary = line.strip.split
matrix << ary
end
matrix.transpose.each do |row|
View Dockerfile
# 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 \
View jst-csv2nt.rb
#!/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
ktym / ajacs55.md
Last active Aug 29, 2015
AJACS 55 Introduction of pathway databases
View ajacs55.md

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。

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
ktym / lodconvert.rb
Last active Aug 29, 2015
RDF format converter
View lodconvert.rb
#!/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
ktym / Sample_ruby_native_apps_script.rb
Created Oct 30, 2014
Ruby port of the BaseSpace Native App test python script
View Sample_ruby_native_apps_script.rb
require 'json'
def metadatajson
json = JSON.parse('
{
"Name": "",
"Description": "",
"HrefAppSession": "",
"Properties": [
{
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