def test_parse_and_submit_params(self):
"""parse_and_submit_params: separates the split-library sequences \
into separate fasta files and posts the sequence data to mg-rast"""
obs = parse_and_submit_params(self.key, self.project_id, self.seq_file, self.output_dir, submit_to_server=False)
self.assertEqual(obs, mg_rast_exp_log)
for i in glob("%s/*" % (self.output_dir)):
self._paths_to_clean_up.append(path.join(self.output_dir, i))
def test_parse_and_submit_params(self):
"""parse_and_submit_params: separates the split-library sequences \
into separate fasta files and posts the sequence data to mg-rast"""
obs=parse_and_submit_params(self.key,self.project_id,self.seq_file,\
self.output_dir,submit_to_server=False)
self.assertEqual(obs, mg_rast_exp_log)
for i in glob('%s/*' % (self.output_dir)):
self._paths_to_clean_up.append(path.join(self.output_dir, i))
def main():
option_parser, opts, args =\
parse_command_line_parameters(**script_info)
# define the variables
project_id = opts.project_id
files = opts.input_fasta_fp
key = opts.web_key_auth
# create directory path
if opts.output_dir:
if exists(opts.output_dir):
output_dir = opts.output_dir
else:
try:
mkdir(opts.output_dir)
output_dir = opts.output_dir
except OSError:
pass
else:
dir_path = './'
# call the main function
log_info = parse_and_submit_params(key, project_id, files, output_dir)
def main():
option_parser, opts, args =\
parse_command_line_parameters(**script_info)
#define the variables
project_id=opts.project_id
files=opts.input_fasta_fp
key = opts.web_key_auth
#create directory path
if opts.output_dir:
if exists(opts.output_dir):
output_dir=opts.output_dir
else:
try:
mkdir(opts.output_dir)
output_dir=opts.output_dir
except OSError:
pass
else:
dir_path='./'
#call the main function
log_info=parse_and_submit_params(key,project_id,files,output_dir)
