mtholder

#!/bin/bash
git rev-list HEAD > commits.txt
prev_ns=0
for sha in $(cat commits.txt)
do
    unix_time=$(git show -s --format=%at "${sha}")
    git checkout $sha || exit
    num_studies=$(find study -name "*.json" | wc -l)
    if test $num_studies -ne $prev_ns
    then

mtholder

#!/usr/bin/env python
import sys
import json
import datetime
synth_j, unix_ts_and_num_studies = sys.argv[1:]
ts_ns = []
with open(unix_ts_and_num_studies, 'r') as inp:
    for line in inp:
        ls = line.strip().split()
        if ls:

mtholder

d = read.table('times_num_studies.tsv', header=TRUE, sep="\t");
print(d);
dt = as.POSIXct(d$time, origin="1970-01-01");
print(dt);

pdf("ot-time-series.pdf");
plot(dt, d$num_phyle_studies,
     xlab="Date", ylab="num studies",
     ylim=c(0, max(d$num_phyle_studies)),
     type="l",

mtholder

#!/bin/bash
OTT_DIR=$1
ROOT_TAXON=$2

echo "Extracting taxa that are descendants of ${ROOT_TAXON}"
otc-taxonomy-parser \
    $OTT_DIR \
    --format="%R | %N |" \
    -r $ROOT_TAXON \
    --cull-flags "major_rank_conflict,major_rank_conflict_inherited,environmental,viral,barren,not_otu,hidden,was_container,inconsistent,hybrid,merged" \

mtholder

#!/usr/bin/env python
import sys
inp = sys.stdin
count = 0
for line in inp:
    ls = [i.strip() for i in line.split(' |')]
    if ls:
        assert len(ls) == 3 and ls[2] == ''
        rank = ls[0]
        if rank == 'species':

mtholder

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:

mtholder

#!/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

#!/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

#!/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

#! /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