本文整理汇总了Python中qiime.util.get_qiime_temp_dir函数的典型用法代码示例。如果您正苦于以下问题:Python get_qiime_temp_dir函数的具体用法?Python get_qiime_temp_dir怎么用?Python get_qiime_temp_dir使用的例子?那么恭喜您, 这里精选的函数代码示例或许可以为您提供帮助。
在下文中一共展示了get_qiime_temp_dir函数的20个代码示例,这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞,您的评价将有助于我们的系统推荐出更棒的Python代码示例。
示例1: setUp
def setUp(self):
self.mapping_file_data = MAPPING_FILE_DATA
self.mapping_file_headers = ['SampleID', 'BarcodeSequence',
'LinkerPrimerSequence', 'Treatment', 'DOB', 'Description']
self.valid_columns = ['Treatment', 'DOB']
self.support_files_filename = get_qiime_temp_dir()
self.support_files_filename_spaces = join(get_qiime_temp_dir(),
'Directory With Spaces/AndNoSpaces')
# data for the custom axes, contains columns that are gradients
self.mapping_file_data_gradient = MAPPING_FILE_DATA_GRADIENT
self.mapping_file_headers_gradient = ['SampleID', 'Treatment', 'Time',
'Weight', 'Description']
self.coords_header = ['PC.355', 'PC.635', 'PC.636', 'PC.354']
self.coords_data = COORDS_DATA
self.coords_eigenvalues = array([1, 2, 3, 4])
self.coords_pct = array([40, 30, 20, 10])
# jackknifed test data
self.jk_mapping_file_headers = ['SampleID', 'C2', 'C3', 'C4']
self.jk_mapping_file_data = [['1', 'a', 'b', 'c'], ['2', 'd', 'e', 'f'],
['3', 'g', 'h', 'i']]
self.jk_coords_header = [['1', '2', '3'], ['1', '2', '3'],
['1', '2', '3'], ['1', '2', '3']]
self.jk_coords_data = [array([[1.2, 0.1, -1.2],[-2.5, -4.0, 4.5]]),
array([[-1.4, 0.05, 1.3],[2.6, 4.1, -4.7]]),
array([[-1.5, 0.05, 1.6],[2.4, 4.0, -4.8]]),
array([[-1.5, 0.05, 1.6],[2.4, 4.0, -4.8]])]
self.jk_coords_eigenvalues = [array([0.80, .11, 0.09]), array([0.76,
.20,0.04]), array([0.84, .14, 0.02]), array([0.84, .11, 0.05])]
self.jk_coords_pcts = [array([0.80, .10, 0.10]), array([0.76, .21,
0.03]), array([0.84, .11, 0.05]), array([0.84, .15, 0.01])]
self.jk_mapping_file_data_gradient = MAPPING_FILE_DATA_GRADIENT
self.jk_mapping_file_headers_gradient = ['SampleID', 'Treatment','Time',
'Weight', 'Description']
self.jk_coords_header_gradient = [['PC.354','PC.355','PC.635','PC.636'],
['PC.354','PC.355','PC.635','PC.636'], ['PC.354','PC.355','PC.635',
'PC.636'], ['PC.354','PC.355','PC.635','PC.636']]
self.jk_coords_data_gradient = [array([[1.2, 0.1, -1.2, 1.1],[-2.5,
-4.0, 4.5, 0.3], [.5, -0.4, 3.5, 1.001], [0.67, 0.23, 1.01, 2.2]]),
array([[1.2, 1, -0.2, 0.1],[-2.5, -4.0, 4.5, 3.2], [.5, -0.4, 3.5,
1.00], [0.57, 0.27, 0.95, 2.1]]), array([[1.0, 1, -1.2, 1.1],[-2.1,
-2.0, 3.5, 0.3], [.5, 3, 3.5, 2], [0.60, 0.33, 1.3, 2.0]]), array([
[1.2, 0.1, -1.2, 1.1],[-2.5,-4.0, 4.5, 0.3], [.5, -0.4, 3.5, 1.001],
[0.69, 0.20, 1.01, 2.2]])]
self.jk_coords_eigenvalues_gradient = [array([0.80, .11, 0.09, 0.0]),
array([0.76, .20,0.04, 0.0]), array([0.84, .14, 0.02, 0.0]), array([
0.84, .11, 0.05, 0.0])]
self.jk_coords_pcts_gradient = [array([0.80, .10, 0.10, 0.0]), array(
[0.76, .21, 0.03, 0.0]), array([0.84, .11, 0.05, 0.0]), array([0.84,
.15, 0.01, 0])]
self.broken_mapping_file_data = BROKEN_MAPPING_FILE
self.broken_mapping_file_data_2_values = BROKEN_MAPPING_FILE_2_VALUES
开发者ID:jessicalmetcalf,项目名称:emperor,代码行数:56,代码来源:test_util.py
示例2: __call__
def __call__(self,
query_fasta_fp,
database_fasta_fp,
output_dir,
observation_metadata_fp=None,
params=None,
HALT_EXEC=False):
if params is None:
params = {}
""" Call the DatabaseMapper """
create_dir(output_dir)
raw_output_fp = self._get_raw_output_fp(output_dir,
params)
output_observation_map_fp = '%s/observation_map.txt' % output_dir
output_biom_fp = '%s/observation_table.biom' % output_dir
log_fp = '%s/observation_table.log' % output_dir
self._assign_dna_reads_to_database(
query_fasta_fp=query_fasta_fp,
database_fasta_fp=database_fasta_fp,
raw_output_fp=raw_output_fp,
temp_dir=get_qiime_temp_dir(),
params=params,
HALT_EXEC=HALT_EXEC)
self._process_raw_output(raw_output_fp,
log_fp,
output_observation_map_fp)
self._generate_biom_output(output_observation_map_fp,
output_biom_fp,
observation_metadata_fp)
开发者ID:AhmedAbdelfattah,项目名称:qiime,代码行数:34,代码来源:map_reads_to_reference.py
示例3: setUp
def setUp(self):
""" """
self.files_to_remove = []
self.dirs_to_remove = []
tmp_dir = get_qiime_temp_dir()
self.test_out = mkdtemp(dir=tmp_dir,
prefix='qiime_parallel_tests_',
suffix='')
self.dirs_to_remove.append(self.test_out)
fd, self.template_fp = mkstemp(dir=self.test_out,
prefix='qiime_template',
suffix='.fasta')
close(fd)
template_f = open(self.template_fp, 'w')
template_f.write(pynast_test1_template_fasta)
template_f.close()
self.files_to_remove.append(self.template_fp)
fd, self.inseqs1_fp = mkstemp(dir=self.test_out,
prefix='qiime_inseqs',
suffix='.fasta')
close(fd)
inseqs1_f = open(self.inseqs1_fp, 'w')
inseqs1_f.write(inseqs1)
inseqs1_f.close()
self.files_to_remove.append(self.inseqs1_fp)
initiate_timeout(60)
开发者ID:Springbudder,项目名称:qiime,代码行数:30,代码来源:test_align_seqs.py
示例4: multiple_file_DA_fitZIG
def multiple_file_DA_fitZIG(input_dir, output_dir, mapping_fp, mapping_category, subcategory_1, subcategory_2):
"""perform metagenomeSeq's Zero Inflated Gaussian (ZIG) OTU differential abundance test on a directory of raw abundance OTU matrices
"""
if not exists(output_dir):
makedirs(output_dir)
file_names = [fname for fname in listdir(input_dir) if not (fname.startswith('.')\
or isdir(fname))]
for fname in file_names:
base_fname, ext = splitext(fname)
original_fname = base_fname+'.biom'
hdf5_infile = join(input_dir, original_fname)
tmp_bt = load_table(hdf5_infile)
tmp_pmf, _ = parse_mapping_file_to_dict(mapping_fp)
check_mapping_file_category(tmp_bt, mapping_fp, mapping_category, subcategory_1, subcategory_2)
tmp_bt.add_metadata(tmp_pmf, 'sample')
#make temporary json biom version - R currently does not have hdf5
outfile = join(output_dir, 'fitZIG_DA_'+base_fname+'.txt')
with tempfile.NamedTemporaryFile(dir=get_qiime_temp_dir(),
prefix='QIIME-differential-abundance-temp-table-',
suffix='.biom') as temp_fh:
temp_fh.write(tmp_bt.to_json('forR'))
temp_fh.flush()
run_fitZIG(temp_fh.name, outfile, mapping_category, subcategory_1, subcategory_2)
开发者ID:ElDeveloper,项目名称:qiime,代码行数:25,代码来源:differential_abundance.py
示例5: test_split_fasta_diff_num_seqs_per_file
def test_split_fasta_diff_num_seqs_per_file(self):
"""split_fasta funcs as expected when diff num seqs go to each file
"""
_, filename_prefix = mkstemp(dir=get_qiime_temp_dir(),
prefix='split_fasta_tests',
suffix='')
close(_)
infile = ['>seq1', 'AACCTTAA', '>seq2', 'TTAACC', 'AATTAA',
'>seq3', 'CCTT--AA']
actual = split_fasta(infile, 2, filename_prefix)
actual_seqs = []
for fp in actual:
actual_seqs += list(open(fp))
remove_files(actual)
expected = ['%s.%d.fasta' % (filename_prefix, i) for i in range(2)]
# list of file paths is as expected
self.assertEqual(actual, expected)
# building seq collections from infile and the split files result in
# equivalent seq collections
self.assertEqual(
LoadSeqs(data=infile, aligned=False),
LoadSeqs(data=actual_seqs, aligned=False))
开发者ID:MicrobiomeResearch,项目名称:qiime,代码行数:25,代码来源:test_split.py
示例6: multiple_file_DA_DESeq2
def multiple_file_DA_DESeq2(input_dir, output_dir, mapping_fp, mapping_category, subcategory_1, subcategory_2, DESeq2_diagnostic_plots):
"""perform DESeq2 negative binomial Wald differential abundance test on a directory of raw abundance OTU matrices
"""
if not exists(output_dir):
makedirs(output_dir)
file_names = [fname for fname in listdir(input_dir) if not (fname.startswith('.')\
or isdir(fname))]
for fname in file_names:
base_fname, ext = splitext(fname)
original_fname = base_fname+'.biom'
hdf5_infile = join(input_dir, original_fname)
tmp_bt = load_table(hdf5_infile)
tmp_pmf, _ = parse_mapping_file_to_dict(mapping_fp)
check_mapping_file_category(tmp_bt, mapping_fp, mapping_category, subcategory_1, subcategory_2)
tmp_bt.add_metadata(tmp_pmf, 'sample')
outfile = join(output_dir, 'DESeq2_DA_'+base_fname+'.txt')
outfile_diagnostic = join(output_dir, 'DESeq2_diagnostic_plots_'+base_fname+'.pdf')
with tempfile.NamedTemporaryFile(dir=get_qiime_temp_dir(),
prefix='QIIME-differential-abundance-temp-table-',
suffix='.biom') as temp_fh:
temp_fh.write(tmp_bt.to_json('forR'))
temp_fh.flush()
run_DESeq2(temp_fh.name, outfile, mapping_category, subcategory_1, subcategory_2, DESeq2_diagnostic_plots, outfile_diagnostic)
开发者ID:ElDeveloper,项目名称:qiime,代码行数:25,代码来源:differential_abundance.py
示例7: setUp
def setUp(self):
self.files_to_remove = []
self.dirs_to_remove = []
# Create example output directory
tmp_dir = get_qiime_temp_dir()
self.test_out = mkdtemp(dir=tmp_dir,
prefix='core_qiime_analyses_test_',
suffix='')
self.dirs_to_remove.append(self.test_out)
# Get input data
self.test_data = get_test_data_fps()
self.qiime_config = load_qiime_config()
self.qiime_config['jobs_to_start'] = 2
self.qiime_config['seconds_to_sleep'] = 1
# suppress stderr during tests (one of the systems calls in the
# workflow prints a warning, and we can't suppress that warning with
# warnings.filterwarnings) here because it comes from within the code
# executed through the system call. Found this trick here:
# http://stackoverflow.com/questions/9949633/suppressing-print-as-stdout-python
self.saved_stderr = sys.stderr
sys.stderr = StringIO()
# Define number of seconds a test can run for before timing out
# and failing
initiate_timeout(600)
开发者ID:Springbudder,项目名称:qiime,代码行数:30,代码来源:test_core_diversity_analyses.py
示例8: setUp
def setUp(self):
""" """
self.files_to_remove = []
self.dirs_to_remove = []
tmp_dir = get_qiime_temp_dir()
self.test_out = get_tmp_filename(tmp_dir=tmp_dir,
prefix='qiime_parallel_tests_',
suffix='',
result_constructor=str)
self.dirs_to_remove.append(self.test_out)
create_dir(self.test_out)
self.template_fp = get_tmp_filename(tmp_dir=self.test_out,
prefix='qiime_template',
suffix='.fasta')
template_f = open(self.template_fp,'w')
template_f.write(pynast_test1_template_fasta)
template_f.close()
self.files_to_remove.append(self.template_fp)
self.inseqs1_fp = get_tmp_filename(tmp_dir=self.test_out,
prefix='qiime_inseqs',
suffix='.fasta')
inseqs1_f = open(self.inseqs1_fp,'w')
inseqs1_f.write(inseqs1)
inseqs1_f.close()
self.files_to_remove.append(self.inseqs1_fp)
initiate_timeout(60)
开发者ID:qiime,项目名称:qp-refactor,代码行数:30,代码来源:test_align_seqs.py
示例9: test_split_fasta_diff_num_seqs_per_file_alt
def test_split_fasta_diff_num_seqs_per_file_alt(self):
"""split_fasta funcs always catches all seqs
"""
# start with 59 seqs (b/c it's prime, so should make more
# confusing splits)
in_seqs = LoadSeqs(data=[('seq%s' % k, 'AACCTTAA') for k in range(59)])
infile = in_seqs.toFasta().split('\n')
# test seqs_per_file from 1 to 1000
for i in range(1, 1000):
_, filename_prefix = mkstemp(dir=get_qiime_temp_dir(),
prefix='split_fasta_tests',
suffix='')
close(_)
actual = split_fasta(infile, i, filename_prefix)
actual_seqs = []
for fp in actual:
actual_seqs += list(open(fp))
# remove the files now, so if the test fails they still get
# cleaned up
remove_files(actual)
# building seq collections from infile and the split files result in
# equivalent seq collections
self.assertEqual(
LoadSeqs(data=infile, aligned=False),
LoadSeqs(data=actual_seqs, aligned=False))
开发者ID:MicrobiomeResearch,项目名称:qiime,代码行数:29,代码来源:test_split.py
示例10: setUp
def setUp(self):
""" """
self.files_to_remove = []
self.dirs_to_remove = []
tmp_dir = get_qiime_temp_dir()
self.test_out = get_tmp_filename(tmp_dir=tmp_dir,
prefix='qiime_parallel_taxonomy_assigner_tests_',
suffix='',
result_constructor=str)
self.dirs_to_remove.append(self.test_out)
create_dir(self.test_out)
self.tmp_seq_filepath = get_tmp_filename(tmp_dir=self.test_out,
prefix='qiime_parallel_taxonomy_assigner_tests_input',
suffix='.fasta')
seq_file = open(self.tmp_seq_filepath, 'w')
seq_file.write(blast_test_seqs.toFasta())
seq_file.close()
self.files_to_remove.append(self.tmp_seq_filepath)
self.id_to_taxonomy_file = NamedTemporaryFile(
prefix='qiime_parallel_taxonomy_assigner_tests_id_to_taxonomy',
suffix='.txt',dir=tmp_dir)
self.id_to_taxonomy_file.write(blast_id_to_taxonomy)
self.id_to_taxonomy_file.seek(0)
self.reference_seqs_file = NamedTemporaryFile(
prefix='qiime_parallel_taxonomy_assigner_tests_ref_seqs',
suffix='.fasta',dir=tmp_dir)
self.reference_seqs_file.write(blast_reference_seqs.toFasta())
self.reference_seqs_file.seek(0)
initiate_timeout(60)
开发者ID:DDomogala3,项目名称:qiime,代码行数:34,代码来源:test_assign_taxonomy.py
示例11: setUp
def setUp(self):
""" """
self.test_data = get_test_data_fps()
self.files_to_remove = []
self.dirs_to_remove = []
# Create example output directory
tmp_dir = get_qiime_temp_dir()
self.test_out = mkdtemp(dir=tmp_dir,
prefix='core_qiime_analyses_test_',
suffix='')
self.dirs_to_remove.append(self.test_out)
self.qiime_config = load_qiime_config()
self.params = parse_qiime_parameters(params_f1)
# suppress stderr during tests (one of the systems calls in the
# workflow prints a warning, and we can't suppress that warning with
# warnings.filterwarnings) here because it comes from within the code
# executed through the system call. Found this trick here:
# http://stackoverflow.com/questions/9949633/suppressing-print-as-stdout-python
self.saved_stderr = sys.stderr
sys.stderr = StringIO()
initiate_timeout(180)
开发者ID:Kleptobismol,项目名称:qiime,代码行数:25,代码来源:test_downstream.py
示例12: setUp
def setUp(self):
"""Defines data that will be used by the tests."""
self.files_to_remove = []
self.dirs_to_remove = []
# Create temp directory to hold input and output.
self.test_dir = mkdtemp(dir=get_qiime_temp_dir(),
prefix='qiime_compare_categories_tests_')
self.dirs_to_remove.append(self.test_dir)
# Create input files under our temp dir.
self.dm_fp = join(self.test_dir, 'dm.txt')
dm_f = open(self.dm_fp, 'w')
dm_f.write(dm_str)
dm_f.close()
self.files_to_remove.append(self.dm_fp)
self.invalid_dm_fp = join(self.test_dir, 'invalid_dm.txt')
invalid_dm_f = open(self.invalid_dm_fp, 'w')
invalid_dm_f.write(invalid_dm_str)
invalid_dm_f.close()
self.files_to_remove.append(self.invalid_dm_fp)
self.map_fp = join(self.test_dir, 'map.txt')
map_f = open(self.map_fp, 'w')
map_f.write(map_str)
map_f.close()
self.files_to_remove.append(self.map_fp)
self.cat_methods = ['adonis', 'anosim', 'mrpp', 'permanova',
'permdisp', 'dbrda']
self.num_methods = ['best', 'morans_i']
self.cat_categories = ['Treatment']
self.num_categories = ['DOB']
self.num_perms = 42
开发者ID:cmhill,项目名称:qiime,代码行数:35,代码来源:test_compare_categories.py
示例13: test_mothur_supported_version
def test_mothur_supported_version(self):
"""mothur is in path and version is supported """
acceptable_version = (1, 25, 0)
self.assertTrue(
which("mothur"),
"mothur not found. This may or may not be a problem depending on "
+ "which components of QIIME you plan to use.",
)
# mothur creates a log file in cwd, so create a tmp and cd there first
log_file = join(get_qiime_temp_dir(), "mothur.log")
command = "mothur \"#set.logfile(name=%s)\" | grep '^mothur v'" % log_file
stdout, stderr, exit_Status = qiime_system_call(command)
# remove log file
remove_files([log_file], error_on_missing=False)
version_string = stdout.strip().split(" ")[1].strip("v.")
try:
version = tuple(map(int, version_string.split(".")))
pass_test = version == acceptable_version
except ValueError:
pass_test = False
version_string = stdout
self.assertTrue(
pass_test,
"Unsupported mothur version. %s is required, but running %s."
% (".".join(map(str, acceptable_version)), version_string),
)
开发者ID:TheSchwa,项目名称:qiime,代码行数:28,代码来源:print_qiime_config.py
示例14: test_temp_dir
def test_temp_dir(self):
"""temp_dir is set to a valid path"""
temp_dir = get_qiime_temp_dir()
self.assertTrue(exists(temp_dir), "temp_dir does not exist: %s" % temp_dir)
self.assertTrue(isdir(temp_dir), "temp_dir is not a directory: %s" % temp_dir)
self.assertTrue(access(temp_dir, W_OK), "temp_dir is not writable: %s" % temp_dir)
开发者ID:TheSchwa,项目名称:qiime,代码行数:7,代码来源:print_qiime_config.py
示例15: setUp
def setUp(self):
self.files_to_remove = []
self.dirs_to_remove = []
# Create example output directory
tmp_dir = get_qiime_temp_dir()
self.test_out = get_tmp_filename(tmp_dir=tmp_dir,
prefix='qiime_parallel_tests_',
suffix='',
result_constructor=str)
self.dirs_to_remove.append(self.test_out)
create_dir(self.test_out)
# Create example input file
self.inseqs1_fp = get_tmp_filename(tmp_dir=self.test_out,
prefix='qiime_inseqs',
suffix='.fasta')
inseqs1_f = open(self.inseqs1_fp,'w')
inseqs1_f.write(inseqs1)
inseqs1_f.close()
self.files_to_remove.append(self.inseqs1_fp)
# Define number of seconds a test can run for before timing out
# and failing
initiate_timeout(60)
开发者ID:B-Rich,项目名称:cmd-abstraction,代码行数:26,代码来源:test_util.py
示例16: setUp
def setUp(self):
""" """
self.files_to_remove = []
self.dirs_to_remove = []
tmp_dir = get_qiime_temp_dir()
self.test_out = mkdtemp(dir=tmp_dir,
prefix='qiime_parallel_blaster_tests_',
suffix='')
self.dirs_to_remove.append(self.test_out)
fd, self.tmp_seq_filepath = mkstemp(dir=self.test_out,
prefix='qiime_parallel_blaster_tests_input',
suffix='.fasta')
close(fd)
seq_file = open(self.tmp_seq_filepath, 'w')
seq_file.write(blast_test_seqs)
seq_file.close()
self.files_to_remove.append(self.tmp_seq_filepath)
self.reference_seqs_file = NamedTemporaryFile(
prefix='qiime_parallel_blaster_tests_ref_seqs',
suffix='.fasta', dir=tmp_dir)
self.reference_seqs_file.write(blast_ref_seqs)
self.reference_seqs_file.seek(0)
initiate_timeout(60)
开发者ID:Kleptobismol,项目名称:qiime,代码行数:27,代码来源:test_blast.py
示例17: _generate_training_files
def _generate_training_files(self):
"""Returns a tuple of file objects suitable for passing to the
RdpTrainer application controller.
"""
tmp_dir = get_qiime_temp_dir()
training_set = RdpTrainingSet()
reference_seqs_file = open(self.Params['reference_sequences_fp'], 'U')
id_to_taxonomy_file = open(self.Params['id_to_taxonomy_fp'], 'U')
for seq_id, seq in MinimalFastaParser(reference_seqs_file):
training_set.add_sequence(seq_id, seq)
for line in id_to_taxonomy_file:
seq_id, lineage_str = map(strip, line.split('\t'))
training_set.add_lineage(seq_id, lineage_str)
training_set.dereplicate_taxa()
rdp_taxonomy_file = NamedTemporaryFile(
prefix='RdpTaxonAssigner_taxonomy_', suffix='.txt', dir=tmp_dir)
rdp_taxonomy_file.write(training_set.get_rdp_taxonomy())
rdp_taxonomy_file.seek(0)
rdp_training_seqs_file = NamedTemporaryFile(
prefix='RdpTaxonAssigner_training_seqs_', suffix='.fasta',
dir=tmp_dir)
for rdp_id, seq in training_set.get_training_seqs():
rdp_training_seqs_file.write('>%s\n%s\n' % (rdp_id, seq))
rdp_training_seqs_file.seek(0)
self._training_set = training_set
return rdp_taxonomy_file, rdp_training_seqs_file
开发者ID:andrea-campisano,项目名称:qiime,代码行数:33,代码来源:assign_taxonomy.py
示例18: setUp
def setUp(self):
"""Define some sample data that will be used by the tests."""
# Standard recipients file with two recipients, one with multiple email
# addresses.
self.recipients = ["# a comment", " ", " foo1\[email protected] ",
"foo2\t [email protected], [email protected],[email protected] "]
# An empty recipients file.
self.empty_recipients = ["# a comment", " ", "\n\t\t\t\t"]
# Standard participants list.
self.participants = ["# a comment", " ", " foo1 ", "foo2"]
# Invalid (duplicate) participants list.
self.duplicate_participants = ["foo1", "foo2", "foo1"]
# The prefix to use for temporary files. This prefix may be added to,
# but all temp dirs and files created by the tests will have this
# prefix at a minimum.
self.prefix = 'my_microbes_tests_'
self.start_dir = getcwd()
self.dirs_to_remove = []
self.files_to_remove = []
self.tmp_dir = get_qiime_temp_dir()
if not exists(self.tmp_dir):
makedirs(self.tmp_dir)
# If test creates the temp dir, also remove it.
self.dirs_to_remove.append(self.tmp_dir)
# Set up temporary input and output directories.
self.output_dir = mkdtemp(dir=self.tmp_dir,
prefix='%soutput_dir_' % self.prefix)
self.dirs_to_remove.append(self.output_dir)
# Set up temporary input and output directories.
self.input_dir = mkdtemp(dir=self.tmp_dir,
prefix='%sinput_dir_' % self.prefix)
self.dirs_to_remove.append(self.input_dir)
# Data that will be used by the tests.
self.otu_cat_sig_gut_fp = join(self.input_dir, 'otu_cat_sig_gut.txt')
otu_cat_sig_gut_f = open(self.otu_cat_sig_gut_fp, 'w')
otu_cat_sig_gut_f.write(otu_cat_sig_gut_text)
otu_cat_sig_gut_f.close()
self.files_to_remove.append(self.otu_cat_sig_gut_fp)
self.otu_cat_sig_palm_fp = join(self.input_dir, 'otu_cat_sig_palm.txt')
otu_cat_sig_palm_f = open(self.otu_cat_sig_palm_fp, 'w')
otu_cat_sig_palm_f.write(otu_cat_sig_gut_text)
otu_cat_sig_palm_f.close()
self.files_to_remove.append(self.otu_cat_sig_palm_fp)
self.rep_seqs_fp = join(self.input_dir, 'rep_seqs.fna')
rep_seqs_f = open(self.rep_seqs_fp, 'w')
rep_seqs_f.write(rep_seqs_text)
rep_seqs_f.close()
self.files_to_remove.append(self.rep_seqs_fp)
开发者ID:ElDeveloper,项目名称:my-microbes,代码行数:59,代码来源:test_format.py
示例19: setUp
def setUp(self):
""" """
self.files_to_remove = []
tmp_dir = get_qiime_temp_dir()
self.test_fp = get_tmp_filename(tmp_dir=tmp_dir,
prefix='bufWriterTest',
suffix='.txt')
self.files_to_remove.append(self.test_fp)
开发者ID:cmhill,项目名称:qiime,代码行数:8,代码来源:test_util.py
示例20: setUp
def setUp(self):
""" """
self.files_to_remove = []
tmp_dir = get_qiime_temp_dir()
fd, self.test_fp = mkstemp(dir=tmp_dir,
prefix='bufWriterTest',
suffix='.txt')
close(fd)
self.files_to_remove.append(self.test_fp)
开发者ID:Gaby1212,项目名称:qiime,代码行数:9,代码来源:test_util.py
注:本文中的qiime.util.get_qiime_temp_dir函数示例由纯净天空整理自Github/MSDocs等源码及文档管理平台,相关代码片段筛选自各路编程大神贡献的开源项目,源码版权归原作者所有,传播和使用请参考对应项目的License;未经允许,请勿转载。 |
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