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#!/bin/env python
__author__ = "Jesse Stombaugh"
__copyright__ = "Copyright 2007-2012, The Cogent Project"
__credits__ = ["Jesse Stombaugh"]
__license__ = "GPL"
__version__ = "1.5.3"
__maintainer__ = "Jesse Stombaugh"
__email__ = "jesse.stombaugh@colorado.edu"
__status__ = "Production"
from os import getcwd, remove, rmdir, mkdir
from os.path import splitext
from cogent.util.unit_test import TestCase, main
from cogent.util.misc import flatten
from random import randint
from cogent.app.guppy import Guppy, build_tree_from_json_using_params
from cogent.app.util import ApplicationError,get_tmp_filename
from cogent.core.tree import PhyloNode
from cogent.parse.tree import DndParser
class Genericguppy(TestCase):
def setUp(self):
'''setup the files for testing guppy'''
# create a list of files to cleanup
self._paths_to_clean_up = []
self._dirs_to_clean_up = []
# get a tmp filename to use
basename=splitext(get_tmp_filename())[0]
# create and write out RAxML stats file
self.json_fname=basename+'.json'
json_out=open(self.json_fname,'w')
json_out.write(JSON_RESULT)
json_out.close()
self._paths_to_clean_up.append(self.json_fname)
def tearDown(self):
"""cleans up all files initially created"""
# remove the tempdir and contents
map(remove,self._paths_to_clean_up)
map(rmdir,self._dirs_to_clean_up)
class guppyTests(Genericguppy):
"""Tests for the guppy application controller"""
def test_guppy(self):
"""Base command-calls"""
app=Guppy()
self.assertEqual(app.BaseCommand, \
''.join(['cd "',getcwd(),'/"; ','guppy']))
app.Parameters['--help'].on()
self.assertEqual(app.BaseCommand, \
''.join(['cd "',getcwd(),'/"; ','guppy --help']))
def test_change_working_dir(self):
"""Change working dir"""
# define working directory for output
working_dir='/tmp/Guppy'
self._dirs_to_clean_up.append(working_dir)
app = Guppy(WorkingDir=working_dir)
self.assertEqual(app.BaseCommand, \
''.join(['cd "','/tmp/Guppy','/"; ','guppy']))
def test_build_tree_from_alignment_using_params(self):
"""Builds a tree from a json file"""
# define working directory for output
outdir='/tmp/'
# set params
params={}
params["tog"] = None
# build tree
tree = build_tree_from_json_using_params(self.json_fname,
output_dir=outdir,
params=params)
self.assertEqual(tree.getNewick(),
DndParser(TREE_RESULT, constructor=PhyloNode).getNewick())
JSON_RESULT="""\
{"tree":
"((seq0000004:0.08408[0],seq0000005:0.13713[1])0.609:0.00215[2],seq0000003:0.02032[3],(seq0000001:0.00014[4],seq0000002:0.00014[5])0.766:0.00015[6]):0[7];",
"placements":
[
{"p":
[[0, -113.210938, 0.713818, 0.064504, 0.000006],
[1, -114.929894, 0.127954, 0.137122, 0.000007],
[2, -114.932766, 0.127587, 0.000008, 0.000006],
[6, -117.743534, 0.007675, 0.000141, 0.027211],
[3, -117.743759, 0.007674, 0.020310, 0.027207],
[4, -117.747386, 0.007646, 0.000131, 0.027266],
[5, -117.747396, 0.007646, 0.000131, 0.027266]
], "n": ["seq0000006"]
},
{"p": [[0, -113.476305, 1.000000, 0.035395, 0.000006]], "n":
["seq0000007"]
}
], "metadata":
{"invocation":
"guppy -t %s -r %s -s %s --out-dir \/tmp %s"
}, "version": 1, "fields":
["edge_num", "likelihood", "like_weight_ratio", "distal_length",
"pendant_length"
]
}
""".replace('\n','').replace(' ','')
TREE_RESULT="""\
((((seq0000004:0.035395,seq0000007:6e-06)\
:0.029109,seq0000006:6e-06)\
:0.019576,seq0000005:0.13713)\
0.609:0.00215,seq0000003:0.02032,(seq0000001:0.00014,seq0000002:0.00014)\
0.766:0.00015)\
:0;
"""
if __name__ == '__main__':
main()
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