Tazro Inutano Ohta inutano

#WeAreHackersWeDance

inutano / moshimokoukouyakyunojoshimanagergaNCBInoSRAwotsukattara.rb

Created May 10, 2011 14:17

counting number of SRA entries which came from same samples.

inutano / nakanidaremoimasenyo.rb

Created May 12, 2011 09:14

explore SRA

	# -- coding: utf-8 --

	require "nokogiri"

	hako = "/path/to/directory_contains_pubmed_html"

	title_list = []
	Dir::entries(hako).each do \|item\|
	if !item.include?("url_list")
	if !item.include?("¥.")

inutano / gist:1570412

Created January 6, 2012 12:36 — forked from yano3/gist:1569121

スキー＠裏磐梯猫魔スキー場

inutano / ar_test.rb

Created January 27, 2012 05:21

てめー　ブッ殺す！　『アクティブ・レコード』ッ！

	require "active_record"

	ActiveRecord::Base.establish_connection(
	:adapter => 'sqlite3',
	:database => './test.sqlite3'
	)

	class UsersInit < ActiveRecord::Migration
	def self.up
	create_table( :users ) do \|t\|

inutano / transfer_speed.sh

Created February 3, 2012 01:17

time sequence raw file transfer speed from NCBI, EBI, DDBJ with various transfer protocol.

	#!/bin/zsh
	#
	# time file transfer from NCBI, EBI, and DDBJ with various transfer protocol.
	# calc avg time send it to stdout
	# usage: transfer_speed.sh <target SRA Run ID>
	# requirement: SRA_Accessions.tab from ftp.ncbi.nlm.nih.gov/sra/reports/Metadata
	#
	###################################################################################

	# time format (set as showing total time by second only)

inutano / AndareInItalia.md

Created February 9, 2012 16:02

( ﾟ∀ﾟ)o彡゜

inutano / MyTumblrTheme(Tetris).html

Created February 11, 2012 08:16 — forked from closer/MyTumblrTheme(Tetris).html

	<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
	"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
	<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
	<head>
	<meta http-equiv="Content-Type" content="text/html; charset=utf-8"/>
	<link rel="icon" href="{Favicon}"/>
	<link rel="alternate" type="application/rss+xml" title="RSS" href="{RSS}"/>
	<title>{Title}{block:PostSummary} - {PostSummary}{/block:PostSummary}</title>
	<style type="text/css">
	* {

inutano / backup.rb

Created February 16, 2012 11:43

backing up the result file

	#!/usr/bin/env ruby
	# -- coding: utf-8 --
	# `gisty sync` to update gist
	# run with --run option to show the whole list of the zip file to be backuped
	# use --test option before running

	# rsync command
	# rsync -avzr iNut@hostname:/home/iNut/project/sra_qualitycheck/result /Volumes/HD2/fastqc2AllSRA

	# get the list of zip files

inutano / nature_parser.rb

Created April 20, 2012 03:55

nature_parser.rb

	# -- coding: utf-8 --

	require "open-uri"
	require "nokogiri"
	require "ap"

	class NatureParser
	def initialize(page_url)
	@nkgr_main = Nokogiri::HTML(open(page_url))
	end

inutano / mickey24dono24.rb

Created May 11, 2012 13:28

	# -- coding: utf-8 --
	require "yaml"
	require "twitter"

	def force_mecab_parse(y_conf, text)
	mecabed = `echo "#{text}" \| /opt/local/bin/mecab`.split("\n")
	parsed_arr = mecabed.map do \|line\|
	tab_sep = line.split("\t")
	com_sep = tab_sep.map{\|p\| p.split(",") }
	com_sep.flatten