def test_write_mapping_file(self):
""" test_write_mapping_file: This function writes a QIIME-formatted
mapping file
"""
# write minimal mapping file
write_mapping_file(0,False,self.output_dir,True)
open_fpath=open(join(self.output_dir,'study_0_run_Fasting_subset_mapping.txt')).read()
# this will return just a mapping file with the header, since
# study 0 is not assigned in the USER_STUDY table
self.assertEqual(open_fpath,exp_mapping)
# write full mapping file
write_mapping_file(0,True,self.output_dir,True)
open_fpath=open(join(self.output_dir,'study_0_run_Fasting_subset_mapping.txt')).read()
# this will return just a mapping file with the header, since
# study 0 is not assigned in the USER_STUDY table
self.assertEqual(open_fpath,exp_full_mapping)
def main():
option_parser, opts, args =\
parse_command_line_parameters(**script_info)
# create output directory
if opts.output_dir:
if path.exists(opts.output_dir):
dir_path=opts.output_dir
else:
try:
makedirs(opts.output_dir)
dir_path=opts.output_dir
except OSError:
pass
else:
dir_path='./'
get_from_test_db=opts.get_from_test_db
study_id=opts.study_id
write_full_mapping=opts.write_full_mapping
run_prefixes=write_mapping_file(study_id,write_full_mapping,dir_path,get_from_test_db)
