Douglas Wu wckdouglas

I have reused the code enough to make a package out of it.

The python package is deposited at Github. with an example in Jupyter notebook.

⚠️ this gist is out-of-date, please see the diffexpr package for a maintained version of the code

	# using starship: https://starship.rs/
	eval "$(starship init zsh)"

	# never beep
	setopt NO_BEEP

	# auto completion: https://dev.to/rossijonas/how-to-set-up-history-based-autocompletion-in-zsh-k7o
	zstyle ':completion:' matcher-list '' 'm:{a-zA-Z}={A-Za-z}' 'r:\|=' 'l:\|=* r:\|=*'
	autoload -U compinit && compinit

	#!/usr/bin/env python

	import subprocess
	from pathlib import Path

	import numpy as np
	import pandas as pd
	import luigi
	from luigi.contrib.sge import SGEJobTask # fixed SGE in this branch https://github.com/wckdouglas/luigi
	from luigi.mock import MockTarget

	# load libraries

	from keras import backend as K
	from keras.models import Sequential, model_from_json
	from keras.layers import Dense, Conv1D,\
	Flatten, MaxPool1D, \
	Dropout, LSTM, \
	Bidirectional
	from sequencing_tools.fastq_tools import reverse_complement, \
	onehot_sequence_encoder

	def make_regions(chromosome_length, how_many_bases_to_look_at):
	start = 0
	end = start + leap
	while end < chromosome_length:
	yield (start, end)
	start = end
	end = end + how_man_bases_to_look_at
	yield (start, chromosome_length)

	>PrefixPE/1
	AATGATACGGCGACCACCGAGATCTACACGTTCAGAGTTCTACAGTCCGACGATC
	>PrefixPE/2
	CAAGCAGAAGACGGCATACGAGATNNNNNNGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT
	>PCR_Primer1
	AATGATACGGCGACCACCGAGATCTACACGTTCAGAGTTCTACAGTCCGACGATC
	>PCR_Primer1_rc
	GATCGTCGGACTGTAGAACTCTGAACGTGTAGATCTCGGTGGTCGCCGTATCATT
	>PCR_Primer2
	CAAGCAGAAGACGGCATACGAGATNNNNNNGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT

	library(grid)

	# http://stackoverflow.com/questions/23588127/match-legend-text-color-in-geom-text-to-symbol
	coloring_legend_text <- function(p){
	g <- ggplotGrob(p)
	names.grobs <- grid.ls(grid.force(g))$name
	labels <- names.grobs[which(grepl("label", names.grobs))]

	# Get the colours
	# The colours are the same as the colours of the plotted points.

	/* Solarized Dark

	For use with Jekyll and Pygments

	http://ethanschoonover.com/solarized

	SOLARIZED HEX ROLE
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	base03 #002b36 background
	base01 #586e75 comments / secondary content