Tazro Inutano Ohta inutano

## cwl-stat.rb
require 'yaml'
require 'json'
require 'pp'

module CWL
  class Workflow
    def initialize(fpath)
      @workflow = YAML.load(open(fpath))
    end

## wtdbg2.console.txt
$ ls ERR2092776_1.fastq
ERR2092776_1.fastq
$ docker run -it --rm -v $(pwd):/work -w /work quay.io/inutano/wtdbg2:v2.2 wtdbg2 -g95m -t 32 -i ERR2092776_1.fastq -fo worm.wtdbg2
--
-- total memory       65880284.0 kB
-- available          65173720.0 kB
-- 12 cores
-- Starting program: wtdbg2 -g95m -t 32 -i ERR2092776_1.fastq -fo worm.wtdbg2
-- pid                         1
-- date         Wed Jul 17 03:38:08 2019

## download.go
// https://golangcode.com/download-a-file-with-progress/
package main

import (
	"fmt"
	"io"
	"net/http"
	"os"
	"strings"

## SAMD00000345.ttl
@base <http://schema.org/> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .

<http://identifiers.org/biosample/SAMD00000345> a <DataRecord>,
    <BioChemEntity>,
    <http://purl.obolibrary.org/obo/OBI_0000747>;
  <additionalProperty> [
    a <PropertyValue>;
    <name> "broad-scale environmental context";
    <value> "n.a."

## SAMD00000345.jsonld
{"@context":{"@base":"http://schema.org/","@vocab":"http://schema.org/","url":{"@type":"http://www.w3.org/2001/XMLSchema#string"},"dateCreated":{"@type":"http://www.w3.org/2001/XMLSchema#dateTime"},"dateModified":{"@type":"http://www.w3.org/2001/XMLSchema#dateTime"},"Sample":{"@id":"http://purl.obolibrary.org/obo/OBI_0000747"},"name":{"@type":"http://www.w3.org/2001/XMLSchema#string"},"value":{"@type":"http://www.w3.org/2001/XMLSchema#string"}},"@type":["DataRecord","BioChemEntity","Sample"],"identifier":"SAMD00000345","dateCreated":"2014-07-30T00:00:00Z","dateModified":"2019-02-18T00:01:52.977Z","isPartOf":{"@type":"Dataset","@id":"https://www.ebi.ac.uk/biosamples/samples"},"datasetPartOf":{"@type":"Dataset","@id":"https://www.ebi.ac.uk/biosamples/samples"},"@id":"http://identifiers.org/biosample/SAMD00000345","name":"SAMD00000345","description":"type strain of Lactobacillus oryzae","url":"https://www.ebi.ac.uk/biosamples/sample/SAMD00000345","additionalProperty":[{"@type":"PropertyValue","name":"INSDC cente

## SAMEA1652233.jsonld
{
  "@context": "http://schema.org",
  "@type": "DataRecord",
  "identifier": "biosamples:SAMEA1652233",
  "dateCreated": "2012-12-31T00:00:00Z",
  "dateModified": "2018-01-20T06:06:51.993Z",
  "mainEntity": {
    "@context": [
      "http://schema.org",
      {

## SAMEA1652233.jsonld
{
  "@context": "http://schema.org",
  "@type": "DataRecord",
  "identifier": "biosamples:SAMEA1652233",
  "dateCreated": "2012-12-31T00:00:00Z",
  "dateModified": "2018-01-20T06:06:51.993Z",
  "mainEntity": {
    "@context": [
      "http://schema.org",
      {

## PRJDB4503.ttl
@prefix bao: <http://www.bioassayontology.org/bao#> .
@prefix biocow: <http://bio.cow/> .
@prefix dcterms: <http://purl.org/dc/terms/> .
@prefix ddbj-tax: <http://ddbj.nig.ac.jp/ontologies/taxonomy/> .
@prefix foaf: <http://xmlns.com/foaf/0.1/> .
@prefix pav: <http://purl.org/pav/> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix sio: <http://semanticscience.org/resource/> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .

## PRJDB4503.json
{
  "@context": "https://me.com/jsonld_bioproject_context.json",
  "URI": "http://identifiers.org/bioproject/PRJDB4503",
  "entry": "biocow:BioProject",
  "Submission": {
    "date_submitted": "2016-01-13",
    "date_last_update": "2016-01-16",
    "access": "public",
    "organization": {
      "organization_name": "Center for Ecological Research, Kyoto University",

## basesPerSite.sh
#!/bin/sh
# Get ID-total sequences from Quanto data set and calculate total

RDF_PORTAL_EP="http://integbio.jp/rdf/sparql"

QUERY=$(
CAT <<'EOF'
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX sos: <http://purl.jp/bio/01/quanto/ontology/sos#>