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John T. Prince jtprince

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jtprince / risk2_saver.rb
Created March 10, 2016 06:23
# Very simple tk application to save progress on Microprose's Risk II game
# (written many years ago)
#
# Create a bat file to run, like this:
# ----save_risk.bat----
# c:\cygwin\bin\rubyw /home/john/risk2_saver.rb c:/Users/john/Desktop/RISK_SAVES
require 'Win32API'
require 'fileutils'
require 'tk'
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jtprince / unique_peptides.rb
Created May 30, 2013 16:12
A simple script that displays unique tryptic peptides for proteins retrieved by uniprot accession number.
#!/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
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jtprince / savgol.rb
Created July 9, 2012 16:13
Savitsky-Golay filter for ruby arrays
# 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
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jtprince / execute_on_modify.rb
Created June 19, 2012 21:13
Uses rb-notify to execute a command when a file has been modified and can sub in the filename into the command
#!/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__)
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jtprince / nil_enumerator.rb
Created June 8, 2012 18:47
NilEnumerator: an enumerator that returns nil instead of a StopIteration exception when it is at the end of the collection
# 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
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jtprince / digestor_spec.rb
Created May 16, 2011 21:46
Digestor Specification
require 'spec/more'
require 'digestor'
describe "Digestor" do
before do
@seq = "MTMDKSELVQKAKLAEQAERYDDMAAAMKAVTEQGHELSNEERNLLSVAYKNVVGARRSSWRVISSIEQKTERNEKKQQMGKEYREKIEAELQDICNDVLELLDKYLIPNATQPESKVFYLKMKGDYFRYLSEVASGDNKQTTVSNSQQAYQEAFEISKKEMQPTHPIRLGLALNFSVFYYEILNSPEKACSLAKTAFDEAIAELDTLNEESYKDSTLIMQLLRDNLTLWTSENQGDEGDAGEGEN"
end
it 'digests a protein' do
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jtprince / lds_general_conference_url_finder.rb
Created May 9, 2010 05:51
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"
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jtprince / xml_name_finder.rb
Created April 14, 2010 00:11
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|
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jtprince / fisher_combine_pvals.py
Created December 11, 2014 23:11
import scipy.stats as sts
from math import log
def fisher_combine_p_values(pvalues):
degrees_freedom = 2*len(pvalues)
summed = sum(-2*log(pval) for pval in pvalues)
return 1.0 - sts.chi2.cdf(summed, degrees_freedom)
#print(fisher_combine_p_values( [0.05, 0.05] ))
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jtprince / quiet boot for arch
Created December 11, 2014 01:27
some notes on quiet boot in arch
# for syslinux, you want something like this:
APPEND root=/dev/sda2 rw vga=current quiet loglevel=0
# OR
APPEND root=/dev/sda2 rw vga=865 quiet loglevel=0
# edit the files systemd-fsck-root.service and systemd-fsck@.service located at /usr/lib/systemd/system/ to configure StandardOutput and StandardError like this:
(...)
[Service]
Type=oneshot