def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
frames = opts.frames
step_size = opts.step_size
output_path = opts.output_dir
input_dir = opts.input_dir
qsub_calls_filepath = opts.qsub_calls_filepath
try:
makedirs(output_path)
except:
pass
for i in range(0,int(frames/(step_size*1.0))):
lower_bound = int((step_size*i)+1)
upper_bound = int(step_size*i+step_size)
filename = 'mathematica_script_%d_%d.m' % (lower_bound, upper_bound)
script_filename = join(output_path, filename)
fd = open(script_filename, 'w')
fd.write(MATHEMATICA_SCRIPT % (frames, input_dir+'/', lower_bound, upper_bound))
fd.close
if qsub_calls_filepath:
fd = open(qsub_calls_filepath, 'a')
fd.write(QSUB_STRING_CMD % (filename, 'MMA_%d_%d' % (lower_bound,
upper_bound)))
fd.close()
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
mapping_fp = opts.mapping_fp
coloring_header_name = opts.coloring_header_name
subject_header_name = opts.subject_header_name
force = opts.force
coords_fp = opts.coords_fp
suppress_trajectory_files = opts.suppress_trajectory_files
sorting_category = opts.sorting_category
if opts.output_path == None:
output_path = 'colored_by_%s_separated_by_%s' % (coloring_header_name,
subject_header_name)
else:
output_path = opts.output_path
try:
makedirs(output_path)
except:
if not force:
option_parser.error('Pfft something bad happened when creating the '
'output directory, try a different --output_path.')
data, headers, _ = parse_mapping_file(open(mapping_fp, 'U'))
subject_index = headers.index(subject_header_name)
coloring_index = headers.index(coloring_header_name)
coloring_values = list(set([row[coloring_index] for row in data]))
@display_wrap
def silly_function(ui):
for c_value in ui.series(coloring_values):
sample_ids = sample_ids_from_metadata_description(open(mapping_fp, 'U'),
'%s:%s' % (coloring_header_name, c_value))
_headers, _data = filter_mapping_file(data, headers, sample_ids, True)
per_color_subject_values = list(set([row[subject_index] for row in _data]))
fd = open(join(output_path, 'color_by_'+c_value+'.txt'), 'w')
for s in ui.series(per_color_subject_values):
fd.write('%s\n' % s)
fd.close()
if not suppress_trajectory_files:
for s in ui.series(per_color_subject_values):
filename = join(output_path, s+'.txt')
if opts.verbose:
print 'Working on printing', filename
COMMAND_CALL = FILTER_CMD % (coords_fp, mapping_fp,
'%s:%s' % (subject_header_name, s), filename,
sorting_category)
o, e, r = qiime_system_call(COMMAND_CALL)
if opts.verbose and e:
print 'Error happened on filtering step: \n%s' % e
continue
COMMAND_CALL = CONVERSION_CMD % (filename, filename)
o, e, r = qiime_system_call(COMMAND_CALL)
if opts.verbose and e:
print 'Error happened on conversion step: \n%s' % e
continue # useless here but just in case
silly_function()