mtholder

#!/bin/sh
for repo in api.opentreeoflife.org deployed-systems gcmdr opentree ot-base oti ott peyotl phylografter taxomachine reference-taxonomy treemachine ;
do
    for suffix in .java .py .sh
    do
        find "$OPEN_TREE_REPO_ROOT/$repo" -name "*$suffix" -exec grep -H $@ {} \; | sed -e "s+$OPEN_TREE_REPO_ROOT/++"
    done
done

mtholder

#!/usr/bin/env python
import sys
from peyotl.api.phylografter import Phylografter
pg = Phylografter()
for study_id in sys.argv[1:]:
    pg.fetch_study(study_id, study_id + '.json')

mtholder

<?xml version="1.0" encoding="UTF-8"?>
<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" targetNamespace="http://www.nexml.org/2009"
	xmlns:xml="http://www.w3.org/XML/1998/namespace" xmlns="http://www.nexml.org/2009"
	xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:sawsdl="http://www.w3.org/ns/sawsdl"
	xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
	xmlns:xhtml="http://www.w3.org/1999/xhtml/datatypes/" elementFormDefault="qualified">

	<!-- <xs:annotation>
		<xs:documentation>
			This module defines annotations that can be attached to

mtholder

#!/usr/bin/env python
import sys
from peyotl.api import APIWrapper
aw = APIWrapper(phylesystem_api_kwargs={'get_from':'api'})
pa = aw.phylesystem_api
o = aw.oti
for line in open(sys.argv[1], 'rU'):
    ls = line.strip()
    if '_' in ls:
        continue

mtholder

#!/usr/bin/env python
import sys
from peyotl.api.taxomachine import Taxomachine
taxomachine = Taxomachine()
from peyotl.nexson_syntax import write_as_json
context_name = 'All life'
for n in sys.argv[1:]:
    if n.startswith('-c'):
        context_name = n[2:]
    else:

mtholder

#!/usr/bin/env python
import sys
from peyotl.api.taxomachine import Taxomachine
taxomachine = Taxomachine()
from peyotl.nexson_syntax import write_as_json
context_name = 'All life'
for n in sys.argv[1:]:
    if n.startswith('-c'):
        context_name = n[2:]
    else:

mtholder

#!/usr/bin/env python
import sys
import os
import re
_SCRIPT_NAME = os.path.split(sys.argv[0])[-1]
_FORBIDDEN = re.compile(r'[^- 0-9a-zA-Z`~@#$%^&*()_+={}|\\\[\]:;"\'<,>.?/]')
_NEEDS_QU_PUNC_STR = r'[\[\]():,;]'
_NEEDS_QUOTES_PATTERN = re.compile(r'(\s|' + _NEEDS_QU_PUNC_STR + ')')
_NEEDS_QUOTES_PUNC_PATTERN = re.compile(_NEEDS_QU_PUNC_STR)
_SINGLE_QUOTE = "'"

mtholder

#!/usr/bin/env python
# vim: set fileencoding=utf-8 :
import sys
import os
import re
u'''
Unicode char lists found by running against ott2.8
Using the names column in taxonomy.tsv required allowing the 
following unicode characters:
    æ denoted: u'\xe6'

mtholder

#!/bin/bash
if ! which ott_names_to_newick.py >/dev/null 2>&1
then 
    echo 'Download ott_names_to_newick.py from https://gist.github.com/mtholder/ac58ab1b3c6a962b9bdc and put it on your PATH'
    exit 1
fi
echo 'grabbing names from taxonomy'
set -x
awk 'BEGIN { FS = "\t\\|\t" } ; {print $3 }' taxonomy.tsv >names.txt
awk 'BEGIN { FS = "\t\\|\t" } ; {print $6 }' taxonomy.tsv >uniqnames.txt

mtholder

#!/usr/bin/env python
import codecs
import sys
chars = set()
for filepath in sys.argv[1:]:
    with codecs.open(filepath, 'r', encoding='utf-8') as fo:
        for line in fo:
            chars.update(iter(line))
c = list(chars)
c.sort()