jtprince

require 'builder'

if ARGV.size == 0
  puts "usage: #{File.basename(__FILE__)} <input>.xml ..."
  puts "output: <input>.result.xml ..."
  exit
end

ARGV.each do |file|
  File.open(file.sub(/\.xml/,'.result.xml'), 'w') do |out|

jtprince

require 'mechanize'

class LDSGeneralConferenceURLFinder
  MONTH_TO_NUM = {
    'April' => 4,
    'October' => 10,
  }

  LDS_ORG = "http://www.lds.org"
  TOC_URL = "http://www.lds.org/conference/display/0,5234,23-1,00.html"

jtprince

#!/usr/bin/ruby

require 'zlib'

NETWORK_FLOAT = 'g*'
NETWORK_DOUBLE = 'G*'
LITTLE_ENDIAN_FLOAT = 'e*'
LITTLE_ENDIAN_DOUBLE = 'E*'
BASE_64 = 'm*'

jtprince

require 'spec/more'
require 'digestor'

describe "Digestor" do

  before do
    @seq = "MTMDKSELVQKAKLAEQAERYDDMAAAMKAVTEQGHELSNEERNLLSVAYKNVVGARRSSWRVISSIEQKTERNEKKQQMGKEYREKIEAELQDICNDVLELLDKYLIPNATQPESKVFYLKMKGDYFRYLSEVASGDNKQTTVSNSQQAYQEAFEISKKEMQPTHPIRLGLALNFSVFYYEILNSPEKACSLAKTAFDEAIAELDTLNEESYKDSTLIMQLLRDNLTLWTSENQGDEGDAGEGEN"
  end

  it 'digests a protein' do

jtprince

# https://gist.github.com/gists/2897543
# NilEnumerator
# 
# an enumerator that yields nil when it is finished.  Only implements #next and
# #peak.  Would only want to use this if your collection does NOT already include
# nils.
# 
# Compare:
#
#     # normal iteration requires catching StopIteration

jtprince

#!/usr/bin/env ruby

# requires rb-inotify (will only work on linux)
require 'rb-inotify'

substitute = '{{}}'
div = '--'

if ARGV.size < 2
  prog = File.basename(__FILE__)

jtprince

# do what the heck you want to public license (see doc end)

# gem install ruby-svg   # provides SVDMatrix
require 'ruby-svd'

class SVDMatrix < Matrix
  def self.[](*rows)
    mat = self.new(rows.size,rows.first.size)
    rows.each_with_index {|row,i| mat.set_row(i, row) }
    mat

jtprince

# http://rosettacode.org/wiki/Twelve_statements

#1.  This is a numbered list of twelve statements.
#2.  Exactly 3 of the last 6 statements are true.
#3.  Exactly 2 of the even-numbered statements are true.
#4.  If statement 5 is true, then statements 6 and 7 are both true.
#5.  The 3 preceding statements are all false.
#6.  Exactly 4 of the odd-numbered statements are true.
#7.  Either statement 2 or 3 is true, but not both.
#8.  If statement 7 is true, then 5 and 6 are both true.

jtprince

#!/usr/bin/env ruby

require 'open-uri'
require 'mspire/digester' # gem install mspire
require 'bio'
require 'set'

accessions = ARGV[0,2]
missed_cleavages = ARGV[2].to_i

jtprince

#!/usr/bin/env ruby
# sc - screenshot utility using imagemagick 'import'

require 'optparse'
require 'ostruct'
require 'shellwords'
require 'fileutils'

viewers = {
  'g' => 'geeqie',