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#!/usr/bin/env python
# test_mothur.py
from __future__ import with_statement
from cStringIO import StringIO
from os import remove, rmdir
from tempfile import mkdtemp, mkstemp
from cogent.util.unit_test import TestCase, main
from cogent.app.mothur import Mothur, mothur_from_file
__author__ = "Kyle Bittinger"
__copyright__ = "Copyright 2007-2009, The Cogent Project"
__credits__ = ["Kyle Bittinger"]
__license__ = "GPL"
__version__ = "1.4.1"
__maintainer__ = "Kyle Bittinger"
__email__ = "kylebittinger@gmail.com"
__status__ = "Prototype"
class MothurTests(TestCase):
def setUp(self):
self.small_fasta = (
'>aaaaaa\nTAGGCTCTGATATAATAGCTCTC---------\n'
'>cccccc\n------------TGACTACGCAT---------\n'
'>bbbbbb\n----TATCGCTTCGACGATTCTCTGATAGAGA\n'
)
self.small_otus = (
'unique\t3\tcccccc\tbbbbbb\taaaaaa\t\n'
'0.62\t2\tbbbbbb,cccccc\taaaaaa\t\n'
'0.67\t1\taaaaaa,bbbbbb,cccccc\t\n'
)
self.small_otus_parsed = [
(float('0'), [['cccccc'], ['bbbbbb'], ['aaaaaa']]),
(float('0.62'), [['bbbbbb', 'cccccc'], ['aaaaaa']]),
(float('0.67'), [['aaaaaa', 'bbbbbb', 'cccccc']]),
]
self.complement_fasta = (
'>a\n--AGGGGTAATAA--\n'
'>b\n--TTATTACCCCT--\n'
'>c\n-------AAAAAA--\n'
)
self.complement_otus = (
'unique\t3\tc\ta\tb\t\n'
'0.50\t2\ta,c\tb\t\n'
'1.00\t1\tb,a,c\t\n'
)
def test_get_help(self):
"""Mothur.getHelp() should return help string"""
expected_help = (
'See manual, available on the MOTHUR wiki:\n'
'http://schloss.micro.umass.edu/mothur/'
)
self.assertEqual(Mothur.getHelp(), expected_help)
def test_compile_mothur_script(self):
"""Mothur._compile_mothur_script() should return valid Mothur script"""
app = Mothur()
app._input_filename = 'test.fasta'
observed_script = app._compile_mothur_script()
expected_script = (
'#unique.seqs(fasta=test.fasta); '
'dist.seqs(fasta=test.unique.fasta); '
'read.dist(column=test.unique.dist, name=test.names); '
'cluster(method=furthest)')
self.assertEqual(observed_script, expected_script)
def test_get_result_paths(self):
"""Mothur._get_result_paths() should guess correct output paths"""
app = Mothur()
app._input_filename = 'test.fasta'
observed_paths = {
'distance matrix': app._derive_dist_path(),
'otu list': app._derive_list_path(),
'rank abundance': app._derive_rank_abundance_path(),
'species abundance': app._derive_species_abundance_path(),
'unique names': app._derive_names_path(),
'unique seqs': app._derive_unique_path(),
}
expected_paths = {
'distance matrix': 'test.unique.dist',
'otu list': 'test.unique.fn.list',
'rank abundance': 'test.unique.fn.rabund',
'species abundance': 'test.unique.fn.sabund',
'unique names': 'test.names',
'unique seqs': 'test.unique.fasta',
}
self.assertEqual(observed_paths, expected_paths)
def test_working_directory(self):
"""Mothur.WorkingDir attribute should not be cast to FilePath object"""
app = Mothur(WorkingDir='/tmp')
self.assertEquals(str(app.WorkingDir), '/tmp')
def test_call_with_multiline_string(self):
"""Mothur.__call__() should return correct otu's for input as single string"""
app = Mothur()
result = app(self.small_fasta)
observed_otus = result['otu list'].read()
self.assertEquals(observed_otus, self.small_otus)
result.cleanUp()
def test_call_with_lines(self):
"""Mothur.__call__() should return correct otu's for input as lines"""
lines = self.small_fasta.split('\n')
app = Mothur(InputHandler='_input_as_lines')
result = app(lines)
observed_otus = result['otu list'].read()
self.assertEquals(observed_otus, self.small_otus)
result.cleanUp()
def test_call_with_path(self):
"""Mothur.__call__() should return correct otu's for input as path"""
working_dir = mkdtemp()
_, filename = mkstemp(dir=working_dir, suffix='.fasta')
with open(filename, 'w') as f:
f.write(self.small_fasta)
app = Mothur(InputHandler='_input_as_path', WorkingDir=working_dir)
result = app(filename)
observed_otus = result['otu list'].read()
self.assertEquals(observed_otus, self.small_otus)
remove(filename)
result.cleanUp()
rmdir(working_dir)
def test_call_with_working_dir(self):
"""Mothur.__call__() should return correct otu's when input dir is changed"""
working_dir = mkdtemp()
app = Mothur(WorkingDir=working_dir)
result = app(self.small_fasta)
observed_otus = result['otu list'].read()
self.assertEquals(observed_otus, self.small_otus)
result.cleanUp()
rmdir(working_dir)
def test_call_with_complement(self):
"""Mothur.__call__() should return correct otu's for input sequences which are reverse complements"""
app = Mothur()
result = app(self.complement_fasta)
observed_otus = result['otu list'].read()
self.assertEquals(observed_otus, self.complement_otus)
result.cleanUp()
def test_mothur_from_file(self):
"""mothur_from_file() should return parsed otus"""
f = StringIO(self.small_fasta)
f.seek(0)
parsed_otus = mothur_from_file(f)
self.assertEquals(parsed_otus, self.small_otus_parsed)
if __name__ == '__main__':
main()
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