misshie’s gists

misshie / percentile.rb

Created April 16, 2024 05:56

Calculate percentaile values in an array of float values

	#!/usr/bin/env ruby
	class Percentile
	ROUND_DIGIT = 1

	def pctile(data0)
	return [] if data0.empty?
	data = data0.map{\|x\|Integer(x.round(ROUND_DIGIT) * (10 ** ROUND_DIGIT))}
	sorted_data = data.sort
	index_sum = Hash.new(0)
	count = Hash.new(0)

misshie / tommo-54kjpn-20230626-GRCh38-gf.additional-header.vcf

Last active November 30, 2023 00:30

	##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description=".">
	##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description=".">
	##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description=".">
	##INFO=<ID=NEGATIVE_TRAIN_SITE,Number=0,Type=Flag,Description=".">
	##INFO=<ID=POSITIVE_TRAIN_SITE,Number=0,Type=Flag,Description=".">
	##INFO=<ID=TOMMO_POSSIBLE_PLATFORM_BIAS_SITE,Number=0,Type=Flag,Description=".">
	##INFO=<ID=CLNREVSTAT,Number=A,Type=String,Description=".">
	##INFO=<ID=CLNSIGCONF,Number=A,Type=String,Description=".">
	##INFO=<ID=CLNDISDBINCL,Number=A,Type=String,Description=".">
	##INFO=<ID=CLNSIGINCL,Number=A,Type=String,Description=".">

misshie / chisq_test.rb

Created October 19, 2023 02:34

2x2 table chi squared test ... use at your own risk ;)

	require 'statistics2'

	def chisq_test(a, b, c, d)
	total = a + b + c + d
	row1_total = a + b
	row2_total = c + d
	col1_total = a + c
	col2_total = b + d
	e_a = (row1_total * col1_total).to_f / total
	e_b = (row1_total * col2_total).to_f / total

misshie / tab2xl.rb

Created April 9, 2020 05:23

A Ruby script conveting a tab delimited text file into an Excel XLSX file using the RubyXL library https://github.com/weshatheleopard/rubyXL

	#!/usr/bin/env ruby
	require 'optparse'
	require 'fileutils'
	require 'rubyXL'
	require 'rubyXL/convenience_methods/cell'
	require 'rubyXL/convenience_methods/color'
	require 'rubyXL/convenience_methods/font'
	require 'rubyXL/convenience_methods/workbook'
	require 'rubyXL/convenience_methods/worksheet'

misshie / parse-duplicated-options.rb

Last active March 28, 2017 03:25

Parse duplicated command-line options into a hash of arrays using Ruby

	#!/usr/bin/env ruby
	# $ ./klass.rb --hoge=fuga --hoge=puyo --foo=bar
	# {:h=>false, :hoge=>["fuga", "puyo"] :foo=>["bar"]}

	require 'optparse'

	class Klass
	attr_reader :opts

	def initialize(opts)

misshie / blink-enclosure.rb

Created October 5, 2016 02:22

Blink all locate LEDs of an SAS-enclosure binded to a block device

	#!/usr/bin/env ruby
	#
	# Blink all locate LEDs of an SAS-enclosure binded to a block device
	# Hiroyuki Mishima ([email protected])
	#

	require 'optparse'

	class BlinkEnclosure
	PARALLEL = "parallel -j1"

misshie / PhysPosGrouping.vb

Last active November 9, 2015 02:59

An Excel VBA macro: Alterternate background of each row according to a key column (column C such as "chr1:123-123;A>T")

	Sub PhysPosGrouping()
	Dim oRange As Range
	Dim lRorB As Long
	Dim lColR As Long
	Dim gcount As Long

	Set oRange = ActiveSheet.UsedRange
	lRowB = oRange.Row + oRange.Rows.Count - 1
	lColR = oRange.Column + oRange.Columns.Count - 1

misshie / byobua

Last active November 8, 2015 23:43

An application sample of "peco" to select attaching byobu session

misshie / qstat2.rb

Last active October 28, 2016 01:56

Modified GridEngine's qstat command showing longer job names

	#!/usr/bin/env ruby
	# License: the MIT lincense.
	# Copyright: MISHIMA, Hiroyuki hmishima at nagasaki-u.ac.jp, 2015

	require 'rexml/document'

	class Qstat2
	JOBNAME_WIDTH = 65

	def initialize

misshie / iupac.rb

Last active August 29, 2015 13:56

The table of IUPAC ambiguous nucleic acid notation

MISHIMA, Hiroyuki misshie