def setUp(self):
self.qiime_config = load_qiime_config()
self.tmp_dir = self.qiime_config['temp_dir'] or '/tmp/'
#Temporary input file
fd, self.tmp_otu_fp = mkstemp(dir=self.tmp_dir,
prefix='R_test_otu_table_',
suffix='.biom')
close(fd)
seq_file = open(self.tmp_otu_fp, 'w')
seq_file.write(test_otu_table)
seq_file.close()
self.tmp_otu_fp_out_CSS = '%s/R_test_otu_table_out_CSS.biom' % (str(
self.tmp_dir))
self.tmp_otu_fp_out_DESeq = '%s/R_test_otu_table_out_DESeq.biom' % (
str(self.tmp_dir))
self.files_to_remove = \
[self.tmp_otu_fp, self.tmp_otu_fp_out_CSS, self.tmp_otu_fp_out_DESeq]
normalize_CSS(self.tmp_otu_fp,
self.tmp_otu_fp_out_CSS,
output_CSS_statistics=False)
normalize_DESeq2(self.tmp_otu_fp,
self.tmp_otu_fp_out_DESeq,
DESeq_negatives_to_zero=False)
def test_normalize_table_DESeq2(self):
normalize_DESeq2(self.tmp_otu_fp,
self.tmp_otu_fp_out_DESeq,
DESeq_negatives_to_zero=False)
input_table = load_table(self.tmp_otu_fp)
output_table = load_table(self.tmp_otu_fp_out_DESeq)
self.compare_tables(input_table, output_table)
def setUp(self):
self.qiime_config = load_qiime_config()
self.tmp_dir = self.qiime_config['temp_dir'] or '/tmp/'
#Temporary input file
fd, self.tmp_otu_fp = mkstemp(dir= self.tmp_dir,
prefix='R_test_otu_table_',
suffix='.biom')
close(fd)
seq_file = open(self.tmp_otu_fp, 'w')
seq_file.write(test_otu_table)
seq_file.close()
self.tmp_otu_fp_out_CSS = '%s/R_test_otu_table_out_CSS.biom' % (str(self.tmp_dir))
self.tmp_otu_fp_out_DESeq = '%s/R_test_otu_table_out_DESeq.biom' % (str(self.tmp_dir))
self.files_to_remove = \
[self.tmp_otu_fp, self.tmp_otu_fp_out_CSS, self.tmp_otu_fp_out_DESeq]
normalize_CSS(self.tmp_otu_fp, self.tmp_otu_fp_out_CSS, output_CSS_statistics=False)
normalize_DESeq2(self.tmp_otu_fp, self.tmp_otu_fp_out_DESeq, DESeq_negatives_to_zero=False)
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
input_path = opts.input_path
out_path = opts.out_path
output_CSS_statistics = opts.output_CSS_statistics
DESeq_negatives_to_zero = opts.DESeq_negatives_to_zero
algorithm = opts.algorithm
list_algorithms = opts.list_algorithms
if list_algorithms:
print 'Available normalization algorithms are:\n%s' % ', '.join(
algorithm_list())
else:
almost_required_options = ['input_path', 'out_path']
for option in almost_required_options:
if getattr(opts, option) is None:
option_parser.error('Required option --%s omitted.' % option)
if algorithm == 'CSS':
if os.path.isdir(input_path):
multiple_file_normalize_CSS(input_path, out_path,
output_CSS_statistics)
elif os.path.isfile(input_path):
normalize_CSS(input_path, out_path, output_CSS_statistics)
else:
# it shouldn't be possible to get here
option_parser.error("Unknown input type: %s" % input_path)
elif algorithm == 'DESeq2':
if os.path.isdir(input_path):
multiple_file_normalize_DESeq2(input_path, out_path,
DESeq_negatives_to_zero)
elif os.path.isfile(input_path):
normalize_DESeq2(input_path, out_path, DESeq_negatives_to_zero)
else:
# it shouldn't be possible to get here
option_parser.error("Unknown input type: %s" % input_path)
else:
# it shouldn't be possible to get here
option_parser.error("Unknown normalization algorithm: %s" %
algorithm)
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
input_path = opts.input_path
out_path = opts.out_path
output_CSS_statistics = opts.output_CSS_statistics
DESeq_negatives_to_zero = opts.DESeq_negatives_to_zero
algorithm = opts.algorithm
list_algorithms = opts.list_algorithms
if list_algorithms:
print 'Available normalization algorithms are:\n%s' % ', '.join(algorithm_list())
else:
almost_required_options = ['input_path', 'out_path']
for option in almost_required_options:
if getattr(opts, option) is None:
option_parser.error('Required option --%s omitted.' % option)
if algorithm == 'CSS':
if os.path.isdir(input_path):
multiple_file_normalize_CSS(input_path, out_path, output_CSS_statistics)
elif os.path.isfile(input_path):
normalize_CSS(input_path, out_path, output_CSS_statistics)
else:
# it shouldn't be possible to get here
option_parser.error("Unknown input type: %s" % input_path)
elif algorithm == 'DESeq2':
if os.path.isdir(input_path):
multiple_file_normalize_DESeq2(input_path, out_path, DESeq_negatives_to_zero)
elif os.path.isfile(input_path):
normalize_DESeq2(input_path, out_path, DESeq_negatives_to_zero)
else:
# it shouldn't be possible to get here
option_parser.error("Unknown input type: %s" % input_path)
else:
# it shouldn't be possible to get here
option_parser.error("Unknown normalization algorithm: %s" % algorithm)
def test_normalize_table_DESeq2(self):
normalize_DESeq2(self.tmp_otu_fp, self.tmp_otu_fp_out_DESeq, DESeq_negatives_to_zero=False)
input_table = load_table(self.tmp_otu_fp)
output_table = load_table(self.tmp_otu_fp_out_DESeq)
self.compare_tables(input_table, output_table)
