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Takatomo Fujisawa tfuji

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tfuji / ncbi_biosample_attributes_extend2ttl.rb
Last active June 27, 2019 13:41
#!/usr/bin/env ruby
require 'nokogiri'
#require 'erb'
require 'pp'
require 'json'
#require 'thor'
# 1. wget https://www.ncbi.nlm.nih.gov/biosample/docs/attributes/?format=xml -O ncbi_biosample_attributes.xml
# 2. %ruby ncbi_biosample_attributes_extend2ttl.rb ncbi_biosample_attributes.xml > biosample_attributes_extend.ttl
@tfuji
tfuji / fetch_context.rb
Last active May 16, 2018 00:23
#require 'open-uri'
require 'rdf/raptor'
require 'json'
require 'json/ld'
require 'pp'
require "faraday"
require 'faraday_middleware'
require 'fileutils'
require 'systemu'
@tfuji
tfuji / ft_rfam.json
Last active June 30, 2016 09:58
Rfam 12.1 to INSDC feature table mapping based on ftp://ftp.ebi.ac.uk/pub/databases/Rfam/11.0/misc/Rfam2INSDC.types
This file has been truncated, but you can view the full file.
{
"RF00001": {
"AC": "RF00001",
"ID": "5S_rRNA",
"DE": "5S ribosomal RNA",
"feature": "rRNA",
"qualifiers": [
{
"product": "5S ribosomal RNA"
},
@tfuji
tfuji / parse_st.rb
Created March 14, 2016 10:59
INSDC structured comment parser
#!/usr/bin/env ruby
require 'rubygems'
require 'bio'
def parse_st_comment comment
tagset_id = nil
tag_name = tag_value = ''
st = Hash.new { |h,k| h[k] = {} }
comment.split("\n").each do |line|
@tfuji
tfuji / genome_reports2ttl.rb
Last active August 29, 2015 14:02
genome_reports2ttl_v2.rb
#!/usr/bin/env ruby
#
# convert genome_reprots to RDF
# * ftp://ftp.ncbi.nlm.nih.gov/genomes/GENOME_REPORTS/prokaryotes.txt
# * ftp://ftp.ncbi.nlm.nih.gov/genomes/GENOME_REPORTS/eukaryotes.txt
#
require 'date'
@tfuji
tfuji / refseq2rdf.rb
Created May 8, 2013 01:41 — forked from ktym/refseq2rdf.rb
#!/usr/bin/env ruby-1.9
require 'rubygems'
require 'bio'
require 'json'
require 'securerandom'
# [TODO] true to combine the result with the EdgeDB
if $DEBUG
$edgedb = true