ktym

#!/usr/bin/env ruby
#
# Mac OS X webarchive is a binary format of a plist file. You can extract the contents manually:
#  1. convert the plist file into XML by "plutil -convert xml1 file.webarchive"
#  2. parse the resulted XML file by some XML parser
#  3. decode "WebResourceData" by Base64.decode64(data) in each key
#  4. save the decoded content into a file indicated by "WebResourceData"
# Thankfully, the plist library can take care of annoying steps 2 and 3.
#
# Preparation:

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 ;

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

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

#!/usr/bin/env ruby                                                                                  

matrix = []

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

matrix.transpose.each do |row|

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-2.3

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

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

ktym

#!/usr/bin/env ruby

require "rubygems"
require "net/http"
require "uri"
require "cgi"
require "json"  # gem install json

class SPARQL

ktym

#!/usr/bin/env ruby
#
# Usage:
#  DAS XML for http://togogenome.org/das/645657/features?segment=NC_017196.1:1,100000 can be generated by
#   % ruby sparql2das.rb 645657 features segment=NC_017196.1:1,100000
#  With ruby -d option, you'll see debug massages with pretty formatted XML (will miss <?xml> tag though)
#
# TODO:
#  Wrap as an Rack app and add X-DAS-* HTTP headers
#

ktym

;;; library

(let ((default-directory "~/lib/lisp"))
 (normal-top-level-add-subdirs-to-load-path))

;; multiple-cursors

; % git clone https://github.com/magnars/multiple-cursors.el.git
; % mv multiple-cursors.el lib/lisp/multiple-cursors