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#! /usr/bin/env python

import dendropy

def get_tree(r):
    tree_str = "((C:1.3,D:4.)34:0.034,(A:1.1,(B:1.2,X:1.6)26:0.026)12:0.0126,E:1.5);"
    tree = dendropy.Tree.get(
            data=tree_str,
            schema="newick",
            rooting=r,

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#!/bin/bash
echo 'This script installs the tools needed for propinquity as subdirectories'
echo 'of the working directory. This assumes that you have a C++ dev environment (g++, boost, automake, libtool)'
echo 'installed. See README files for propinquity and otcetera if those builds fail'
echo 'Also assumes virtualenv for python'

CONTEXT_DIR="${PWD}"
virtualenv propinquity-env
source propinquity-env/bin/activate

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#!/usr/bin/env python
from collections import defaultdict
import dendropy
import sys
import os
_SCRIPT_NAME = os.path.split(sys.argv[0])[-1]
def error(msg):
    sys.stderr.write('{}: Error: {}\n'.format(_SCRIPT_NAME, msg))

OUT = sys.stdout

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#!/usr/bin/env python
import sys
import os
import json
import codecs
dn = sys.argv[1]
outfn = sys.argv[2]
d = {}
for s in os.listdir(dn):
  if s.endswith('.out'):

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#!/usr/bin/env
import sys

'''
python gen-curl-oti.py template.txt studies.txt
where studies.txt is the list of studies used in synthesis.
  and template is a cURL call with XYZ inplace of the study id (and no other XYZ)
cURL
'''

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#!/usr/bin/env python
import sys
import re

inp = sys.stdin
outp = sys.stdout

JS_PAT = re.compile(r'^<script src="/opentree/static/(.+)" type="text/javascript"></script>\s+$')
CSS_PAT = re.compile(r'^<link href="/opentree/static/(.+)" rel="stylesheet" type="text/css" />\s+$')

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#!/usr/bin/env python
from dendropy import DnaCharacterMatrix, Tree
import sys
d = DnaCharacterMatrix.get(path=sys.argv[1],
                           schema='fasta')
# make the taxon_namespace immutable, so the tree does not add
#   new labels...
d.taxon_namespace.is_mutable = False
tree = Tree.get(path=sys.argv[2],
                schema='newick',

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#!/usr/bin/env python
from StringIO import StringIO
import sys

out = sys.stdout
def get_indented(x, indent):
    start_indent = indent
    written_something = False
    out = StringIO()
    for letter in x:

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/* Most of this code is from GBParsy which available from https://code.google.com/p/gbfp/

T.-H. Lee, Y.-K. Kim and B.H. Nahm (2008) GBParsy: A GenBank flatfile parser library with high speed. BMC Bioinformatics, 9:321.

That code is released under the GPL (see bottom of file).


Mark T. Holder only wrote the slight modification to parsing of the GI and a simpliefied main 
function (based on the example seqext.c from gbfpy)

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()