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Toshiaki Katayama ktym

  • Database Center for Life Science
  • Japan
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View rdf-config-metastanza-test.json
[
{
"refex_id": "RFX0000113860",
"ex_value": "7.4464837623184",
"see_also": "http://www.ncbi.nlm.nih.gov/gene/308",
"RefExSample": "http://refex.dbcls.jp/sample/RES00000436",
"sample_id": "RES00000436",
"taxonomy": "http://identifiers.org/taxonomy/9606",
"age": "21",
"stage": "adult",
View 404.json
{
"head": {
"link": [],
"vars": [
"hgnc_uri",
"gene_symbol",
"approved_name",
"chromosomal_location",
"alias",
"ncbigene",
@ktym
ktym / unwebarchive.rb
Created Feb 12, 2013
Extract contents of a .webarchive file.
View unwebarchive.rb
#!/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:
View idorg-ontology-dblink.owl
View hint.graphql
"""
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
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 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 \