misshie

MONDO International: unique labels before OWL-to-OBO conversion

This gist contains a SPARQL Update script and a Docker wrapper for ROBOT. Together they preprocess the MONDO International Edition OWL file so that ROBOT can emit a structurally valid OBO file.

The OBO format requires a 1-to-1 mapping for the name tag (derived from rdfs:label). The international OWL file can have multiple labels per term (translations, obsolete legacy names, and imported-ontology redundancies), so a direct conversion fails with "multiple name tags not allowed". This pipeline removes those conflicts. Multilingual strings and leftover duplicate labels are relocated; original labels on obsolete terms are dropped rather than kept as synonyms.

Files

• preprocess_labels_for_obo.ru — SPARQL Update run by ROBOT
• run-docker-robot.sh — pulls obolibrary/robot and runs the conversion

misshie

;; Explicitly copy/paste between the kill-ring and x-clipboard
;; using the xlip command
;; C-c y : yank from x-clipboard
;; C-c c : copy from kill-ring to x-clipboard

(setq x-select-enable-clipboard nil)
(setq x-select-enable-primary nil)
(defun yank-from-x-clipboard()
  "Yank from X clipboard using xclip."
  (interactive)

misshie

#!/usr/bin/env ruby
require 'oj'

class MyHandler
  # see Oj::ScHandler
  def hash_start       ; {}    ; end
  def hash_end                 ; end
  def array_start      ; []    ; end
  def array_end                ; end
  def add_value(value) ; value ; end

misshie

#!/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

##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

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

#!/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

#!/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

#!/usr/bin/env ruby
#
# Blink all locate LEDs of an SAS-enclosure binded to a block device
# Hiroyuki Mishima (missy@be.to)
#

require 'optparse'

class BlinkEnclosure
  PARALLEL = "parallel -j1"

misshie

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