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BioInformatics Week 2016 Kanazawa

3月は金沢近郊で研究会がたくさんあります

• 国内版BioHackathon BH15.15
  • http://wiki.lifesciencedb.jp/mw/BH15.15
• 第20回 オープンバイオ研究会
  • http://open-bio.jp/?meeting20
• SIG-MBI
• http://www.sigmbi.jp/

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#!/bin/bash
#
# get-dra.sh ver 0.1.2 by [email protected]
# usable only in DDBJ supercomputer system
#
# usage:
#   get-dra.sh <SRA Experiment ID or SRA Run ID> <Output directory>
#
set -eu

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#!/bin/bash

MY_GROUP="ec2-user"
if [ "$MY_GROUP" = "" ] ; then
  echo '!!! undefined variable MY_GROUP.'
  echo '!!!'
  echo '!!! ex.) MY_GROUP=staff'
  echo '!!!'
  exit 1
fi

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Documentation of Whole-SRA-FastQC

code: Quanto

Software

Totally based on FastQC

Version

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#!/bin/zsh
#
# usage: 
#   convert.sh experimentList.tab SRA_Accessions.tab
#
#   SRA_Accessions.tab is available at ftp.ncbi.nlm.nih.gov/sra/reports/Metadata/SRA_Accessions.tab
#
set -e

# variables

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#!/bin/bash

MY_GROUP="ec2-user"

if [ "$MY_GROUP" = "" ] ; then
  echo '!!! undefined variable MY_GROUP.'
  echo '!!!'
  echo '!!! ex.) MY_GROUP=staff'
  echo '!!!'
  exit 1

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# :)

require 'json'

if __FILE__ == $0
  data = open(ARGV.first).read.split("\n")
  
  # remove unnecessary lines
  download_at = data.shift
  blank_line  = data.shift

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require 'nokogiri'

def get_fpath(type, format, runid, expid, subid)
  case type
  when :ftp
    case format
    when :fastq
      File.join(
        "ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/fastq",
        subid.sub(/...$/,""),

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#!/usr/bin/env ruby

require 'nokogiri'
require 'erb'
#require 'uri'
#require 'pp'

class BioSampleSet

	include Enumerable

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# :)

require 'nokogiri'
require 'ap'
require 'json'

desc "parse all.xml"
task :parse do |t|
  pubmedset = Nokogiri::XML(open("./all.xml")).css("ArticleId").select{|n| n.attr("IdType").to_s == "pmc" }.map{|n| n.inner_text }
  puts pubmedset