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#!/usr/bin/env python
# test_dotur.py
from os import getcwd, remove, rmdir, mkdir, path
import tempfile, shutil
from cogent.core.moltype import DNA, RNA, PROTEIN
from cogent.core.sequence import DnaSequence, RnaSequence
from cogent.core.alignment import DataError
from cogent.util.unit_test import TestCase, main
from cogent.util.misc import flatten
from cogent.app.dotur import Dotur, dotur_from_alignment, dotur_from_file,\
remap_seq_names
from cogent.parse.dotur import OtuListParser
__author__ = "Jeremy Widmann"
__copyright__ = "Copyright 2007-2009, The Cogent Project"
__credits__ = ["Jeremy Widmann"]
__license__ = "GPL"
__version__ = "1.4.1"
__maintainer__ = "Jeremy Widmann"
__email__ = "jeremy.widmann@colorado.edu"
__status__ = "Development"
def rna_distance(first,second):
first = RnaSequence(first)
return first.fracDiff(second)
class DoturTests(TestCase):
def setUp(self):
"""Dotur general setUp method for all tests"""
self.seqs1_unaligned = {'1':'ACUGCUAGCUAGUAGCGUACGUA',\
'2':'GCUACGUAGCUAC',\
'3':'GCGGCUAUUAGAUCGUA'}
self.seqs2_aligned = {'a': 'UAGGCUCUGAUAUAAUAGCUCUC---------',\
'c': '------------UGACUACGCAU---------',\
'b': '----UAUCGCUUCGACGAUUCUCUGAUAGAGA'}
self.seqs2_unaligned = {'a': 'UAGGCUCUGAUAUAAUAGCUCUC',\
'c': 'UGACUACGCAU',\
'b': 'UAUCGCUUCGACGAUUCUCUGAUAGAGA'}
#self.seqs1 aligned to self.seqs2 with self.seqs2 included.
self.seqs1_and_seqs2_aligned = \
{'a': 'UAGGCUCUGAUAUAAUAGC-UCUC---------',\
'b': '----UAUCGCUUCGACGAU-UCUCUGAUAGAGA',\
'c': '------------UGACUAC-GCAU---------',\
'1': '-ACUGCUAGCUAGUAGCGUACGUA---------',\
'2': '----------GCUACGUAG-CUAC---------',\
'3': '-----GCGGCUAUUAG-AU-CGUA---------',\
}
self.otu_list_string = \
"""unique 3 a b c
0.00 3 a b c
0.59 2 a,c b
0.78 1 a,c,b
"""
self.otu_res_list = [
[0.0,3,[['a'],['b'],['c']]],\
[0.0,3,[['a'],['b'],['c']]],\
[float(0.59),2,[['a','c'],['b']]],\
[float(0.78),1,[['a','c','b']]],\
]
self.distance_matrix_string = \
"""
3
a 0.0 0.78125 0.59375
b 0.78125 0.0 0.71875
c 0.59375 0.71875 0.0
"""
self.int_keys = {'seq_1': 'b', 'seq_0': 'a', 'seq_2': 'c'}
self.otu_lists_unmapped = [\
[['seq_0'], ['seq_1'], ['seq_2']],
[['seq_0'], ['seq_1'], ['seq_2']],
[['seq_0', 'seq_2'], ['seq_1']],
[['seq_0', 'seq_2', 'seq_1']],
]
self.otu_lists_mapped = [\
[['a'], ['b'], ['c']],
[['a'], ['b'], ['c']],
[['a', 'c'], ['b']],
[['a', 'c', 'b']],
]
self.temp_dir = tempfile.mkdtemp()
self.temp_dir_spaces = '/tmp/test_for_dotur/'
try:
mkdir(self.temp_dir_spaces)
except OSError:
pass
try:
#create sequence files
f = open(path.join(self.temp_dir, 'seqs1.sto'),'w')
f.write('')
f.close()
self.d_mat_file = path.join(self.temp_dir, 'dmat.txt')
d_mat = open(self.d_mat_file,'w')
d_mat.write(self.distance_matrix_string)
d_mat.close()
except OSError:
pass
def test_base_command(self):
"""Dotur BaseCommand should return the correct BaseCommand"""
c = Dotur()
self.assertEqual(c.BaseCommand,\
''.join(['cd "',getcwd(),'/"; ','dotur']))
c.Parameters['-l'].on()
self.assertEqual(c.BaseCommand,\
''.join(['cd "',getcwd(),'/"; ','dotur -l']))
def test_changing_working_dir(self):
"""Dotur BaseCommand should change according to WorkingDir"""
c = Dotur(WorkingDir='/tmp/dotur_test')
self.assertEqual(c.BaseCommand,\
''.join(['cd "','/tmp/dotur_test','/"; ','dotur']))
c = Dotur()
c.WorkingDir = '/tmp/dotur_test2'
self.assertEqual(c.BaseCommand,\
''.join(['cd "','/tmp/dotur_test2','/"; ','dotur']))
#removing the dirs is proof that they were created at the same time
#if the dirs are not there, an OSError will be raised
rmdir('/tmp/dotur_test')
rmdir('/tmp/dotur_test2')
def test_remap_seq_names(self):
"""remap_seq_names should function as expected."""
for unmapped, mapped in zip(self.otu_lists_unmapped,\
self.otu_lists_mapped):
self.assertEqual(remap_seq_names(unmapped,self.int_keys),mapped)
def test_dotur_from_alignment(self):
"""dotur_from_alignment should behave correctly."""
res = dotur_from_alignment(aln=self.seqs2_aligned,moltype=RNA,\
distance_function=rna_distance)
self.assertEqual(res,self.otu_res_list)
def test_dotur_from_file(self):
"""dotur_from_alignment should behave correctly."""
res = dotur_from_file(self.d_mat_file)
self.assertEqual(res,self.otu_res_list)
def test_general_cleanUp(self):
"""Last test executed: cleans up all files initially created"""
# remove the tempdir and contents
shutil.rmtree(self.temp_dir)
shutil.rmtree(self.temp_dir_spaces)
if __name__ == '__main__':
main()
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