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

#!/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

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

#!/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

#!/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

#!/bin/bash

# works on the unpacked dir that is posted under the link 
#    text "All pipeline outputs " on the release page.
# E.g. the release page https://tree.opentreeoflife.org/about/synthesis-release/v9.1
#    points to http://files.opentreeoflife.org/synthesis/opentree9.1/opentree9.1_output.tgz
#    as its versions of "All pipeline outputs"
#
# I downloaded that, unpacked it, and provide the path to that dir as the only
#    argument to this script.

mtholder

\documentclass{article}
\usepackage{amsmath}
\usepackage{paralist}
\DeclareMathOperator*{\argmin}{argmin}
\begin{document}
\section*{Note on detecting whether a pattern is parsimony informative}
Let $\ell(T, c)$ be the unordered parsimony length of discrete character pattern $c$ on 
tree $T$ and $\ell(T, c, i)$ be the parsimony length that combination of pattern and tree
 when state $i$ is  enforced as the state for the root of the tree.
Data pattern $c$ is ``parsimony informative'' if and only if, 

mtholder

#!/usr/bin/env python
import sys
try:
    annot_fp = sys.argv[1]
except:
    sys.exit("Expecting a path to an annotations.json file as the only argument.\n")
import json
import codecs
with codecs.open(annot_fp, 'rU', encoding='utf-8') as inp:
    obj = json.load(inp)

mtholder

#!/bin/bash

cd ~
mkdir OpenTree
cd OpenTree/
git clone https://github.com/mtholder/propinquity.git

echo '[opentree]' > ~/.opentree
echo "home = $PWD" >> ~/.opentree
echo 'peyotl = %(home)s/peyotl' >> ~/.opentree

mtholder

#!/usr/bin/env python
from __future__ import print_function
from peyotl.api import PhylesystemAPI
import sys
studyid = sys.argv[1]

phy = PhylesystemAPI(get_from='local')
nx = phy.get_study(studyid)['data']['nexml']
print(nx.keys())