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_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_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_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_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_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_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_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_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 __call__(self, seq_path, result_path=None, log_path=None):
"""Returns dict mapping {otu_id:[seq_ids]} for each otu.
Parameters:
seq_path: path to file of sequences
result_path: path to file of results. If specified, should
dump the result to the desired path instead of returning it.
log_path: path to log, which should include dump of params.
"""
app = Mothur(InputHandler='_input_as_path')
app.Parameters['method'].on(self.Params['Algorithm'])
results = app(seq_path)
parsed_otus = mothur_parse(results['otu list'])
clusters = self.__pick_clusters(parsed_otus)
results.cleanUp()
# From here down, this is all copied straight from
# CdHitOtuPicker, and prime for refactoring into a private
# method of OtuPicker
if result_path:
# if the user provided a result_path, write the
# results to file with one tab-separated line per
# cluster
of = open(result_path, 'w')
for i, cluster in enumerate(clusters):
of.write('%s\t%s\n' % (i, '\t'.join(cluster)))
of.close()
result = None
log_str = 'Result path: %s' % result_path
else:
# if the user did not provide a result_path, store
# the clusters in a dict of {otu_id:[seq_ids]}, where
# otu_id is arbitrary
result = dict(enumerate(clusters))
log_str = 'Result path: None, returned as dict.'
if log_path:
# if the user provided a log file path, log the run
log_file = open(log_path, 'w')
log_file.write(str(self))
log_file.write('\n')
log_file.write('%s\n' % log_str)
# return the result (note this is None if the data was
# written to file)
return result
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_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)
