mtholder

#!/bin/bash
inpdir=$1
if ! test -d "${inpdir}" ; then
	echo "$0 must be passed in a directory of subproblems (with ott###.tre files)."
	exit 1
fi
rpwd=`realpath .`
rpid=`realpath $inpdir`
if test "${rpwd}" = "${rpid}" ; then
	echo "$0 Cannot be run in place."

mtholder

#!/usr/bin/env python3
'''Reverses the order of the first n-1 lines of a file
and writes it to stdout.
'''
import sys
fp = sys.argv[1]
with open(fp, 'r', encoding='utf-8') as inp:
    lines = inp.readlines()
last = lines.pop(-1)
lines.reverse()

mtholder

#!/bin/env python
import json
import sys
import subprocess
import itertools


inpjson = 'subproblem_size_summary.json'
with open(inpjson, 'r', encoding='utf-8') as inp:
    summary_blob = json.load(inp)

mtholder

#!/bin/env python
import json
import sys
import subprocess
import itertools

DEBUG = False

def count_tips_and_inf_splits(fn):
    out = subprocess.check_output(['otc-degree-distribution', fn], stderr=subprocess.DEVNULL).decode('utf-8')

mtholder

#!/bin/bash

otc-tree-tool --indented-table labelled_supertree/labelled_supertree_simplified_ottnames.tre > subproblems/indented-table.txt
cat subproblems/indented-table.txt | sed -E '/ +mrca/d' | sed -E 's/.* ott([0-9]+) : ([0-9]+)/"ott\1": \2,/' > num_tips_for_ott_internals_in_labelled_tree.json
rm subproblems/indented-table.txt

mtholder

#!/bin/bash
# This needs to be made part of the propinquity process.
# 	MTH ran steps that made up the basis of this before the
#	Jan 2020 SSB workshop. So the resulting file will be in
#	the https://files.opentreeoflife.org/synthesis/opentree12.3/opentree12.3/subproblems/
#	folder, but (perversely enough) not in the tar archive at https://files.opentreeoflife.org/synthesis/opentree12.3/opentree12.3.tgz
# If all goes as planned, we'll start adding this to the tree build process so that it will be in 
#	builds and archives made after 12.3

# This is to be run with the working directory being the propinquity

mtholder

#!/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

#!/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

#!/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

#!/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'