1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
|
#!/bin/env python
from os import getcwd, remove, rmdir, mkdir
from cogent.util.unit_test import TestCase, main
from cogent.util.misc import flatten
from cogent.app.raxml import Raxml,raxml_alignment, build_tree_from_alignment
from cogent.app.util import ApplicationError
from cogent.parse.phylip import get_align_for_phylip
from cogent.core.tree import PhyloNode
from cogent.core.moltype import RNA
from StringIO import StringIO
__author__ = "Micah Hamady"
__copyright__ = "Copyright 2007-2009, The Cogent Project"
__credits__ = ["Micah Hamady", "Rob Knight", "Daniel McDonald"]
__license__ = "GPL"
__version__ = "1.4.1"
__maintainer__ = "Micah Hamady"
__email__ = "Micah Hamady"
__status__ = "Development"
class GenericRaxml(TestCase):
def setUp(self):
"""Setup data for raxml tests"""
self.seqs1 = ['ACUGCUAGCUAGUAGCGUACGUA','GCUACGUAGCUAC',
'GCGGCUAUUAGAUCGUA']
self.labels1 = ['>1','>2','>3']
self.lines1 = flatten(zip(self.labels1,self.seqs1))
self.test_model = "GTRCAT"
self.align1 = get_align_for_phylip(StringIO(PHYLIP_FILE))
self.test_fn1 = "/tmp/raxml_test1.txt"
self.test_fn2 = "raxml_test1.txt"
self.test_fn1_space = "/tmp/raxml test1.txt"
def writeTmp(self, outname):
"""Write data to temp file"""
t = open(outname, "w+")
t.write(PHYLIP_FILE)
t.close()
class RaxmlTests(GenericRaxml):
"""Tests for the Raxml application controller"""
def test_raxml(self):
"""raxml BaseCommand should return the correct BaseCommand"""
r = Raxml()
self.assertEqual(r.BaseCommand, \
''.join(['cd \"',getcwd(),'/\"; ','raxmlHPC -e 0.1 -f d -c 50']))
r.Parameters['-s'].on('seq.nexus')
self.assertEqual(r.BaseCommand,\
''.join(['cd \"',getcwd(),'/\"; ',\
'raxmlHPC -e 0.1 -f d -c 50 -s seq.nexus']))
def test_raxml_params(self):
"""raxml should raise exception if missing required params"""
r = Raxml(WorkingDir="/tmp")
r.SuppressStdout = True
r.SuppressStderr = True
# raise error by default
self.assertRaises(ValueError, r)
# specify output name
r.Parameters['-n'].on("test_name")
self.assertRaises(ApplicationError, r)
# specify model
r.Parameters['-m'].on("GTRCAT")
self.assertRaises(ApplicationError, r)
r.Parameters['-s'].on(self.test_fn1)
self.assertRaises(ApplicationError, r)
self.writeTmp(self.test_fn1)
o = r()
o.cleanUp()
remove(self.test_fn1)
def test_raxml_from_file(self):
"""raxml should run correctly using filename"""
r = Raxml(WorkingDir="/tmp")
r.Parameters['-s'].on(self.test_fn1)
r.Parameters['-m'].on("GTRCAT")
r.Parameters['-n'].on("test_me")
# test with abs filename
cur_out = self.test_fn1
self.writeTmp(cur_out)
out = r()
out.cleanUp()
remove(cur_out)
# test with rel + working dir
r.Parameters['-s'].on(self.test_fn2)
r.Parameters['-n'].on("test_me2")
r.Parameters['-w'].on("/tmp/")
self.writeTmp(self.test_fn1)
out = r()
out.cleanUp()
remove(self.test_fn1)
r.Parameters['-s'].on("\"%s\"" % self.test_fn1_space)
r.Parameters['-n'].on("test_me3")
r.Parameters['-w'].on("/tmp/")
#print r.BaseCommand
self.writeTmp(self.test_fn1_space)
out = r()
out.cleanUp()
remove(self.test_fn1_space)
def test_raxml_alignment(self):
"""raxml_alignment should work as expected"""
phy_node, parsimony_phy_node, log_likelihood, total_exec \
= raxml_alignment(self.align1)
def test_build_tree_from_alignment(self):
"""Builds a tree from an alignment"""
tree = build_tree_from_alignment(self.align1, RNA, False)
self.assertTrue(isinstance(tree, PhyloNode))
self.assertEqual(len(tree.tips()), 7)
self.assertRaises(NotImplementedError, build_tree_from_alignment, \
self.align1, RNA, True)
PHYLIP_FILE= """ 7 50
Species001 UGCAUGUCAG UAUAGCUUUA GUGAAACUGC GAAUGGCUCA UUAAAUCAGU
Species002 UGCAUGUCAG UAUAGCUUUA GUGAAACUGC GAAUGGCUNN UUAAAUCAGU
Species003 UGCAUGUCAG UAUAGCAUUA GUGAAACUGC GAAUGGCUCA UUAAAUCAGU
Species004 UCCAUGUCAG UAUAACUUUG GUGAAACUGC GAAUGGCUCA UUAAAUCAGG
Species005 NNNNNNNNNN UAUAUCUUAU GUGAAACUUC GAAUGCCUCA UUAAAUCAGU
Species006 UGCAUGUCAG UAUAGCUUUG GUGAAACUGC GAAUGGCUCA UUAAAUCAGU
Species007 UGCAUGUCAG UAUAACUUUG GUGAAACUGC GAAUGGCUCA UUAAAUCAGU
"""
if __name__ == '__main__':
main()
|
