dpmccabe’s gists

dpmccabe / course_code_sort.R

Last active May 30, 2018 20:26

course code sorting

	library(dplyr)
	library(tidyr)
	library(stringr)

	sort_course_codes <- function(course_codes) {
	course_with_sorting <- data_frame(course_code = course_codes) %>%
	mutate(course_code_cleaned = str_trim(tolower(str_replace_all(
	course_code, "[(\\[\\{][^(\\[\\{]+[)\\]\\}]", ""
	)))) %>%
	separate(

dpmccabe / syntax.r

Created May 31, 2017 15:36

	merged_fit <- alply(1:n_samp, 1, function(s) {
	h_seg_dat_new$h.capseg.d[[merge_ixs[1]]] <- unlist(h_seg_dat_new$h.capseg.d[merge_ixs])
	h_seg_dat_new$h.capseg.raw[[merge_ixs[1]]] <- unlist(h_seg_dat_new$h.capseg.raw[merge_ixs])
	h_seg_dat_new$h.capseg.annot[[merge_ixs[1]]]$pos <- unlist(lapply(h_seg_dat_new$h.capseg.annot[merge_ixs], "[[", "pos"))
	h_seg_dat_new$gh.wes.allele.d[[merge_ixs[1]]] <- do.call(cbind, h_seg_dat_new$gh.wes.allele.d[merge_ixs])
	h_seg_dat_new$gh.wes.allele.annot[[merge_ixs[1]]]$pos <- unlist(lapply(h_seg_dat_new$gh.wes.allele.annot[merge_ixs], "[[", "pos"))
	if (n_merge_hets >= 2) h_seg_dat_new$seg_phase_pr[[merge_ixs[1]]] <- 0.5
	if (n_merge_hets >= 2) h_seg_dat_new$consensus_phase[[merge_ixs[1]]] <- init_merged_consensus_phase(log_het_phase_prob_list)
	capture_em_fit_new$log.het.phase.prob[[merge_ixs[1]]] <- data_frame("x1" = rep(NA, n_merge_hets))
	capture_em_fit_new$het.phase.prob[[merge_ixs[1]]] <- capture_em_fit_new$log.het.phase.prob[[merge_ixs[1]]]

dpmccabe / gist:8b4208c1cc98998fbc508592426364f9

Created April 12, 2017 21:16

	17:13:34.819 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/xchip/scarter/dmccabe/software/gatk-protected_e54dac3/build/libs/gatk-protected-package-e54dac3-SNAPSHOT-local.jar!/com/intel/gkl/native/libgkl_compression.so
	[April 12, 2017 5:13:34 PM EDT] org.broadinstitute.hellbender.tools.exome.convertbed.ConvertBedToTargetFile --input test2.bed --output test2.target --help false --version false --showHidden false --verbosity INFO --QUIET false --use_jdk_deflater false --use_jdk_inflater false
	[April 12, 2017 5:13:34 PM EDT] Executing as [email protected] on Linux 2.6.32-642.13.1.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_121-b13; Version: Version:e54dac3-SNAPSHOT
	17:13:34.858 INFO ConvertBedToTargetFile - Defaults.BUFFER_SIZE : 131072
	17:13:34.858 INFO ConvertBedToTargetFile - Defaults.COMPRESSION_LEVEL : 5
	17:13:34.858 INFO ConvertBedToTargetFile - Defaults.CREATE_INDEX : false
	17:13:34.858 INFO ConvertBedToTargetFile - Defaults.CREATE_MD5 : false
	17

dpmccabe / CIEDE2000.R

Last active January 23, 2017 16:56

CIEDE2000 color difference algorithm

	kL <- 1
	kC <- 1
	kH <- 1
	K1 <- 0.045
	K2 <- 0.015

	# x and y should be two different colors in Lab* space
	CIEDE2000 <- function(x, y) {
	L1 <- x$L
	L2 <- y$L

dpmccabe / snippets.sh

Last active September 15, 2016 16:59

bash snippets

	###########################################################################################################################
	# commands
	###########################################################################################################################

	# ls only file size and name
	stat -c "%s %n" *.txt \| column -t

	# watch output of qstat, highlight changes every 5s
	watch -n 5 -d 'qstat'

dpmccabe / backtrace

Created May 20, 2015 20:47

	ArgumentError at /api/v1/products/components_and_accessories
	============================================================

	> When assigning attributes, you must pass a hash as an argument.

	app/controllers/api/v1/products_controller.rb, line 7
	-----------------------------------------------------

	``` ruby
	2 before_filter :verify_auth_token

dpmccabe / make_password.applescript

Last active January 23, 2017 16:58

	set x to ""
	repeat 12 times
	set x to x & some item of "abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ12345678901234567890"
	end repeat
	set the clipboard to x

	tell application "System Events"
	keystroke "v" using {command down}
	end tell

dpmccabe / build_and_clean.py

Created October 1, 2014 04:09

clean temporary files after latexing build

	import sublime, sublime_plugin
	from os.path import dirname, realpath
	import subprocess

	class BuildAndClean(sublime_plugin.TextCommand):
	def run(self, edit):
	self.view.window().run_command("build")
	sublime.set_timeout_async(self.clean, 3000)

	def clean(self):

dpmccabe / field_with_error.rb

Last active August 29, 2015 14:05 — forked from t2/application.rb

add file as initializer

	ActionView::Base.field_error_proc = Proc.new do \|html_tag, instance\|
	html = %(<span class="has-error">#{html_tag}</span>).html_safe
	form_fields = %w(textarea input select)
	element = Nokogiri::HTML::DocumentFragment.parse(html_tag).css(['label', form_fields].join(', ')).first

	if element.node_name.eql?('label')
	html = %(<span class='has-error'>#{element}</span>).html_safe
	elsif form_fields.include?(element.node_name)
	html = %(<span class='has-error'>#{element}<span class='help-block'>#{[instance.error_message].join(', ')}</span></span>).html_safe
	end

dpmccabe / gist:c53aeecc2b4c7b23e6c8

Created July 9, 2014 19:20

	$ rails g spree_account_recurring:install /Users/devin/.rbenv/versions/2.1.2/lib/ruby/gems/2.1.0/gems/activerecord-4.1.4/lib/active_record/dynamic_matchers.rb:26:in `method_missing': undefined method `preference' for Spree::Recurring(Table doesn't exist):Class (NoMethodError)
	from /Users/devin/.rbenv/versions/2.1.2/lib/ruby/gems/2.1.0/bundler/gems/spree-account-recurring-d9977b380f05/app/models/spree/recurring.rb:7:in `<class:Recurring>'
	from /Users/devin/.rbenv/versions/2.1.2/lib/ruby/gems/2.1.0/bundler/gems/spree-account-recurring-d9977b380f05/app/models/spree/recurring.rb:2:in `<module:Spree>'
	from /Users/devin/.rbenv/versions/2.1.2/lib/ruby/gems/2.1.0/bundler/gems/spree-account-recurring-d9977b380f05/app/models/spree/recurring.rb:1:in `<top (required)>'
	from /Users/devin/.rbenv/versions/2.1.2/lib/ruby/gems/2.1.0/gems/activesupport-4.1.4/lib/

Devin McCabe dpmccabe