def test_raise_error_on_parallel_unavailable(self):
"""raise_error_on_parallel_unavailable functions as expected """
self.assertRaises(RuntimeError,raise_error_on_parallel_unavailable,{})
self.assertRaises(RuntimeError,raise_error_on_parallel_unavailable,\
{'jobs_to_start':'1'})
raise_error_on_parallel_unavailable({'jobs_to_start':'2'})
raise_error_on_parallel_unavailable({'jobs_to_start':'24'})
def test_raise_error_on_parallel_unavailable(self):
"""raise_error_on_parallel_unavailable functions as expected """
self.assertRaises(RuntimeError, raise_error_on_parallel_unavailable,
{})
self.assertRaises(RuntimeError,raise_error_on_parallel_unavailable,\
{'jobs_to_start':'1'})
raise_error_on_parallel_unavailable({'jobs_to_start': '2'})
raise_error_on_parallel_unavailable({'jobs_to_start': '24'})
def main():
option_parser, opts, args =\
parse_command_line_parameters(**script_info)
study_id = opts.study_id
for i in range(1,25):
output_dir='/home/wwwdevuser/user_data/studies/study_%s/processed_data_%s/' % (study_id,i)
if not exists(output_dir):
break
else:
continue
print output_dir
sff_fname=opts.sff_fname
map_fname = opts.map_fname
verbose = opts.verbose
print_only = opts.print_only
parallel = opts.parallel
denoise=opts.denoise
if parallel:
raise_error_on_parallel_unavailable()
try:
parameter_f = open(opts.parameter_fp)
except IOError:
raise IOError,\
"Can't open parameters file (%s). Does it exist? Do you have read access?"\
% opts.parameter_fp
try:
makedirs(output_dir)
except OSError:
if opts.force:
pass
else:
# Since the analysis can take quite a while, I put this check
# in to help users avoid overwriting previous output.
print "Output directory already exists. Please choose "+\
"a different directory, or force overwrite with -f."
exit(1)
if print_only:
command_handler = print_commands
else:
command_handler = web_app_call_commands_serially
if verbose:
status_update_callback = print_to_stdout
else:
status_update_callback = no_status_updates
run_process_sff_through_pick_otus(sff_input_fp=sff_fname,\
mapping_fp=map_fname,\
output_dir=output_dir,\
denoise=denoise,\
command_handler=command_handler,\
params=parse_qiime_parameters(parameter_f),\
qiime_config=qiime_config,\
parallel=parallel,\
status_update_callback=status_update_callback)
def main():
option_parser, opts, args =\
parse_command_line_parameters(**script_info)
fasta_file = opts.split_lib_seqs
verbose = opts.verbose
print_only = opts.print_only
parallel = opts.parallel
output_dir=opts.output_dir
if output_dir:
if exists(output_dir):
dir_path=output_dir
else:
try:
mkdir(output_dir)
dir_path=output_dir
except OSError:
pass
else:
dir_path='./'
if parallel:
raise_error_on_parallel_unavailable()
try:
parameter_f = open(opts.parameter_fp)
except IOError:
raise IOError,\
"Can't open parameters file (%s). Does it exist? Do you have read access?"\
% opts.parameter_fp
try:
makedirs(dir_path)
except OSError:
if opts.force:
pass
else:
# Since the analysis can take quite a while, I put this check
# in to help users avoid overwriting previous output.
print "Output directory already exists. Please choose "+\
"a different directory, or force overwrite with -f."
exit(1)
if print_only:
command_handler = print_commands
else:
command_handler = web_app_call_commands_serially
if verbose:
status_update_callback = print_to_stdout
else:
status_update_callback = no_status_updates
new_output_dir=join(dir_path,'chain_picked_otus')
create_dir(new_output_dir)
run_chain_pick_otus(fasta_file=fasta_file,\
output_dir=new_output_dir,\
command_handler=command_handler,\
params=parse_qiime_parameters(parameter_f),\
qiime_config=qiime_config,\
parallel=parallel,\
status_update_callback=status_update_callback)
