mtholder’s gists

mtholder / suppress-non-listed-ids-or-unnamed.py

Created December 28, 2019 19:14

suppresses nodes from an OT tree if they do not have an ID listed in a separate file. Takes newick-tree-filepath and file-with-ids-one-per-line as args

	#!/bin/env python3
	import sys
	import dendropy
	import re
	id_extractor = re.compile('.*ott([0-9]+)$')
	tree_filepath = sys.argv[1]
	id_filepath = sys.argv[2]
	tree = dendropy.Tree.get(path=tree_filepath, schema='newick', suppress_internal_node_taxa=False)

	# Get the list of IDs to retain

mtholder / ott_ids_for_nexson.sh

Created December 12, 2019 00:08

takes a path to an Open Tree NexSON. writes a element of python dict mapping the filename to a frozenset of mapped OTT Ids

	#!/bin/bash
	fp=$1
	fn=$(basename $fp)
	if ! test -f $fp ; then
	echo "$fp does not exist"
	exit 1
	fi
	o=`grep '"^ot:ottId": ' "$fp" \| sed 's/".*": //' \| sort -g \| sed ':a;N;$!ba;s/\n/ /g' \| sed -E 's/ +/ /g'`
	echo "\"${fn}\": frozenset([ ${o} ]),"

mtholder / construct_c_trie.py

Created June 7, 2019 22:55

start of generating a C-trie in python

	#!/usr/bin/env python3
	# -- coding: <encoding name> --
	from __future__ import print_function
	from collections import defaultdict
	from math import log
	import codecs
	from ctypes import c_uint64 as c_trie_node_type
	import sys

	""" Pseudocode from Maly, 1976 Appendix B

mtholder / crawl.py

Last active October 19, 2018 20:40 — forked from bredelings/crawl.py

Silly web crawler

	#!/usr/bin/python3

	import requests
	import time
	from threading import Thread

	machine='http://localhost:1984'
	# machine='https://ot39.opentreeoflife.org'
	# machine='https://api.opentreeoflife.org'

mtholder / crontest.sh

Created August 9, 2018 18:22

cron-executable script (no output except in case of failure) for testing Open Tree services

	#!/bin/bash
	PAR_DIR=/home/mholder
	TEST_OT_DIR="${PAR_DIR}/test-ot-ws"
	TEST_LOG_DIR="${PAR_DIR}/testotlogs"
	source "${PAR_DIR}/env/test-otc-ws/bin/activate" \|\| exit
	source "${TEST_OT_DIR}/dev/activate.sh" \|\| exit
	cd "${TEST_OT_DIR}" \|\| exit
	date > "${TEST_LOG_DIR}/latest.log"
	nf=0
	if ! git pull origin >> "${TEST_LOG_DIR}/latest.log" 2>&1 ; then

mtholder / brent_opt.py

Created April 21, 2018 13:40

simple demo of using bracket and brent to optimize a single-variable function

	#! /usr/bin/env python
	# -- coding: utf-8 --
	from scipy.optimize import bracket, brent
	from scipy.stats import binom
	from math import log, isnan
	import sys

	_inf = float('inf')
	def main():
	n = 100

mtholder / scrape_rb_tutorial_download_as_archive.py

Created March 2, 2018 23:21

brittle scrape of download archive from rb tutorial

	#!/usr/bin/env python
	from __future__ import print_function
	import sys
	try:
	from selenium import webdriver
	except:
	sys.exit('Need to run:\npip install selenium\n')
	import tempfile
	import time
	import os

mtholder / buneman_four_point_condition_tree.py

Last active October 25, 2017 15:55

takes 6 (non-negative) distances as arguments (in the order [d12, d13, d14, d23, d24, d34]) and returns tree (with branch lengths if the four-point condition is met).

	#!/usr/bin/env python
	from __future__ import print_function
	import sys
	try:
	farg = [float(i) for i in sys.argv[1:]]
	for i in farg:
	assert i >= 0.0
	d_12, d_13, d_14, d_23, d_24, d_34 = farg
	except:
	m = 'd_12, d_13, d_14, d_23, d_24, d_34'

mtholder / tnt2nexus.py

Created July 6, 2017 02:47

brittle script for converting a TNT output to NEXUS trees block. I'm not sure what the TNT name quoting rules are, so it reads the first ws delim word in the xread block to get the names

	#!/usr/bin/env python
	import sys
	import os
	import re
	tread_pat = re.compile('^tread')
	xread_pat = re.compile('^xread')
	treefilename = sys.argv[1]
	ext_data_pref = "tread 'tree(s) from TNT, for data in "

mtholder / remap_2_to_col_ids_to_third.py

Created May 17, 2017 21:53

	import sys
	fn = sys.argv[1]
	ls_list = []
	mapping = {}
	with open(fn, 'r') as inp:
	for n, line in enumerate(inp):
	ls = line.split('\t\|\t')
	assert len(ls) == 5
	assert ls[-1] == '\n'
	if n > 0:

Mark T. Holder mtholder