Chris Tomkins-Tinch tomkinsc

## graphical_mpileup_qual.py
#!/usr/bin/env python

import re, sys, os
from stat import S_ISFIFO
import argparse

# quick and dirty script to show emoji or bars for samtools mpileup quality scrores
# extra verbose so this does not require any external libraries
# based on fastqe and emojify:
    # https://raw.githubusercontent.com/fastqe/fastqe/master/fastqe/fastqe_map.py

## gist:f5d52274226139887380480543063f6a
||id.google.com^
||accounts.google.com/gsi/$3p

## flowcell-id_to_seqmodel.py
#!/usr/bin/env python

import sys, re

flowcell_to_machine_model_and_chemistry = {
    r'[A-Z,0-9]{5}AAXX':{
        "machine":    "Illumina Genome Analyzer IIx",
        "chemistry":  "All",
        "lane_count":  8,
        "note":       ""

## mask_seqs_at_positions.py
#!/usr/bin/env python

import sys, os
import argparse
from Bio import SeqIO
from Bio.Seq import MutableSeq, Seq
from Bio.SeqIO import FastaIO
from itertools import cycle, chain


## outlet_state.sh
#!/bin/bash

# This gets the state of Meross outlets, model MSS110. It may only work if the outlets have been added via HomeKit but not accessed via the Meross cloud.
# requires jq
# see Meross API:
#   https://github.com/dieantu/ha-config/blob/96cd122bcb6e0559e147c57d04448828cbc190d5/custom_components/meross_lan/merossclient/api.http

PLUG_IP=$1
PLUG_STATE=$2
currenttime="$(date '+%s')"

## count_words_after_heading_google_docs_script.js
//var delimitRegex = /\W+/;
//var delimitRegex = /[^\w\n]+/;
var delimitRegex = /[^\w\-\–\—\(\)\.:,;]+/;

function countPerSection() {
  var body = DocumentApp.getActiveDocument().getBody();
  var para = body.getParagraphs();
  var levels = para.map(function(p) {
    return [DocumentApp.ParagraphHeading.TITLE,
            DocumentApp.ParagraphHeading.SUBTITLE,

## export_excel_from_graphpad.py
#!/usr/bin/env python

import os
import glob
import pandas as pd
import pzfx_parser as gpp # pip install pzfx_parser; conda install openpyxl

gp_ext = ".pzfx"

for f in glob.glob(f"./*{gp_ext}"):

## make_tree.sh
#!/bin/bash

set -e -o pipefail

DEPENDENCIES=(iqtree mafft trimal curl python)

if ! $(hash $DEPENDENCIES &> /dev/null); then
    echo "ERROR! aborting..."
    echo "The following need to be installed and on the PATH:"
    for dependency in ${DEPENDENCIES[@]}; do

## download_fasta_by_accession.sh
#!/bin/bash

curl http://www.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucest&rettype=fasta&id=NC_045512.2 > NC_045512.2.fasta

## matplotlib_colorcycler_colorblind_friendly.py
# matplotlib color cycler using Okabe & Ito's palette
#   https://jfly.uni-koeln.de/color/
# later mentioned by Bang Wong:
#   https://www.nature.com/articles/nmeth.1618
# re-order colors as desired for the application
c = cycler(color=[
    (0,0,0), # black
    (230/255, 159/255, 0/255), # orange
    (86/255, 180/255, 233/255), # sky blue
    (0/255, 158/255, 115/255), # blueish green
	#!/usr/bin/env python

	import re, sys, os
	from stat import S_ISFIFO
	import argparse

	# quick and dirty script to show emoji or bars for samtools mpileup quality scrores
	# extra verbose so this does not require any external libraries
	# based on fastqe and emojify:
	# https://raw.githubusercontent.com/fastqe/fastqe/master/fastqe/fastqe_map.py
	#!/usr/bin/env python

	import sys, re

	flowcell_to_machine_model_and_chemistry = {
	r'[A-Z,0-9]{5}AAXX':{
	"machine": "Illumina Genome Analyzer IIx",
	"chemistry": "All",
	"lane_count": 8,
	"note": ""
	#!/usr/bin/env python

	import sys, os
	import argparse
	from Bio import SeqIO
	from Bio.Seq import MutableSeq, Seq
	from Bio.SeqIO import FastaIO
	from itertools import cycle, chain
	#!/bin/bash

	# This gets the state of Meross outlets, model MSS110. It may only work if the outlets have been added via HomeKit but not accessed via the Meross cloud.
	# requires jq
	# see Meross API:
	# https://github.com/dieantu/ha-config/blob/96cd122bcb6e0559e147c57d04448828cbc190d5/custom_components/meross_lan/merossclient/api.http

	PLUG_IP=$1
	PLUG_STATE=$2
	currenttime="$(date '+%s')"
	//var delimitRegex = /\W+/;
	//var delimitRegex = /[^\w\n]+/;
	var delimitRegex = /[^\w\-\–\—\(\)\.:,;]+/;

	function countPerSection() {
	var body = DocumentApp.getActiveDocument().getBody();
	var para = body.getParagraphs();
	var levels = para.map(function(p) {
	return [DocumentApp.ParagraphHeading.TITLE,
	DocumentApp.ParagraphHeading.SUBTITLE,
	#!/usr/bin/env python

	import os
	import glob
	import pandas as pd
	import pzfx_parser as gpp # pip install pzfx_parser; conda install openpyxl

	gp_ext = ".pzfx"

	for f in glob.glob(f"./*{gp_ext}"):
	#!/bin/bash

	set -e -o pipefail

	DEPENDENCIES=(iqtree mafft trimal curl python)

	if ! $(hash $DEPENDENCIES &> /dev/null); then
	echo "ERROR! aborting..."
	echo "The following need to be installed and on the PATH:"
	for dependency in ${DEPENDENCIES[@]}; do
	#!/bin/bash

	curl http://www.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucest&rettype=fasta&id=NC_045512.2 > NC_045512.2.fasta
	# matplotlib color cycler using Okabe & Ito's palette
	# https://jfly.uni-koeln.de/color/
	# later mentioned by Bang Wong:
	# https://www.nature.com/articles/nmeth.1618
	# re-order colors as desired for the application
	c = cycler(color=[
	(0,0,0), # black
	(230/255, 159/255, 0/255), # orange
	(86/255, 180/255, 233/255), # sky blue
	(0/255, 158/255, 115/255), # blueish green