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View cwl-stat.rb
require 'yaml'
require 'json'
require 'pp'
module CWL
class Workflow
def initialize(fpath)
@workflow = YAML.load(open(fpath))
end
@inutano
inutano / wtdbg2.console.txt
Created Jul 25, 2019
wtdbg2 genome assembly: output in console
View 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
View download.go
// https://golangcode.com/download-a-file-with-progress/
package main
import (
"fmt"
"io"
"net/http"
"os"
"strings"
View 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."
View 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
View 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",
{
View 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",
{
View 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#> .
View 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",
View 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#>
You can’t perform that action at this time.