def _run(self, data):
output_choice = 'display'
(boolean_var, fileupload_parameters) = utils.get_boolean_file_params(service_dir+'/' + tool.replace('-','_') +'.yml')
exclude = fileupload_parameters + ['content-type']
for x in fileupload_parameters:
exclude = exclude + [x + '_string', x + '_string_type']
command = utils.perl_scripts + '/' + tool
result_dir = utils.make_tmp_dir(tool)
for param in data:
if param in boolean_var:
if data[param] == True:
command += ' -' + param
elif data[param] == False:
continue
elif data[param] is not None and data[param] != '' and param not in exclude:
if 'uth_' in param:
uth_type = param.split('_', 1)
command += ' -uth ' + uth_type[1] + ' ' + str(data[param])
elif 'lth_' in param:
lth_type = param.split('_', 1)
command += ' -lth ' + lth_type[1] + ' ' + str(data[param])
else:
command += ' -' + param + ' ' + str(data[param])
command += utils.parse_fileupload_parameters(data, fileupload_parameters, tool, result_dir, ',')
return utils.run_command(command, output_choice, tool, 'text', result_dir)
def parse_arg(self, code, parser):
tmp_dir = make_tmp_dir(self._data_dir)
js_path = hash_val(code) + '.js'
js_path = os.path.join(tmp_dir, js_path)
write(js_path, code)
ast_path = parser.parse(js_path)
return tmp_dir, ast_path
def _run(self, data):
output_choice = 'display'
(boolean_var, fileupload_parameters) = utils.get_boolean_file_params(service_dir+'/' + tool.replace('-','_') +'.yml')
exclude = fileupload_parameters + ['content-type']
for x in fileupload_parameters:
exclude = exclude + [x + '_string', x + '_string_type']
exclude += ['markov_order']
command = utils.rsat_bin + '/' + tool
result_dir = utils.make_tmp_dir(tool)
for param in data:
if param in boolean_var:
if data[param] == True:
command += ' -' + param
elif data[param] == False:
continue
elif data[param] is not None and data[param] != '' and param not in exclude:
if param == 'org' and data[param] is not None and data[param] != '':
len = 1
if 'markov_order' in data and data['markov_order'] is not None and data['markov_order'] != '':
len = data['markov_order'] + 1
command += ' -bgfile ' + utils.get_backgroundfile(data['org'], len) + '.gz'
elif 'uth_' in param:
uth_type = param.split('_', 1)
command += ' -uth ' + uth_type[1] + ' ' + str(data[param])
elif 'lth_' in param:
lth_type = param.split('_', 1)
command += ' -lth ' + lth_type[1] + ' ' + str(data[param])
else:
command += ' -' + param + ' ' + str(data[param])
command += utils.parse_fileupload_parameters(data, fileupload_parameters, tool, result_dir, ',')
return utils.run_command(command, output_choice, tool, 'ft', result_dir)
def _run(self, data):
output_choice = 'display'
(boolean_var, fileupload_parameters
) = utils.get_boolean_file_params(service_dir + '/' +
tool.replace('-', '_') + '.yml')
exclude = fileupload_parameters + ['content-type']
for x in fileupload_parameters:
exclude = exclude + [x + '_string', x + '_string_type']
command = utils.perl_scripts + '/' + tool
result_dir = utils.make_tmp_dir(tool)
for param in data:
if param in boolean_var:
if data[param] == True:
command += ' -' + param
elif data[param] == False:
continue
elif data[param] is not None and data[
param] != '' and param not in exclude:
command += ' -' + param + ' ' + str(data[param])
command += utils.parse_fileupload_parameters(data,
fileupload_parameters,
tool, result_dir, ',')
command += ' -o ' + result_dir + '/position_analysis.tab'
return utils.run_command_background(command, tool, result_dir,
'position_analysis_index.html')
def _run(self, data):
output_choice = 'display'
(boolean_var, fileupload_parameters
) = utils.get_boolean_file_params(service_dir + '/' +
tool.replace('-', '_') + '.yml')
exclude = fileupload_parameters + ['content-type']
for x in fileupload_parameters:
exclude = exclude + [x + '_string', x + '_string_type']
command = utils.perl_scripts + '/' + tool
result_dir = utils.make_tmp_dir(tool)
for param in data:
if param in boolean_var:
if data[param] == True:
command += ' -' + param
elif data[param] == False:
continue
elif data[param] is not None and data[
param] != '' and param not in exclude:
if param == 'return':
return_fields = data[param].split(',')
for i in return_fields:
command += ' -return ' + i.strip()
elif param == 'q':
q_fields = data[param].split(',')
for i in q_fields:
command += ' -q ' + i.strip()
else:
command += ' -' + param + ' ' + str(data[param])
command += utils.parse_fileupload_parameters(data,
fileupload_parameters,
tool, result_dir, ',')
return utils.run_command(command, output_choice, tool, 'tab',
result_dir)
def _run(self, data):
output_choice = 'display'
(boolean_var, fileupload_parameters
) = utils.get_boolean_file_params(service_dir + '/' +
tool.replace('-', '_') + '.yml')
exclude = fileupload_parameters + ['content-type']
for x in fileupload_parameters:
exclude = exclude + [x + '_string', x + '_string_type']
command = utils.rsat_bin + '/' + tool
result_dir = utils.make_tmp_dir(tool)
options_var = [
'maxspacing', 'minspacing', 'sites', 'collect', 'seedmatrix',
'strand'
]
for param in data:
if param in boolean_var:
if data[param] == True:
if param == 'zoops':
command += ' --zoops'
else:
command += ' -' + param
elif data[param] == False:
continue
elif data[param] is not None and data[
param] != '' and param not in exclude:
if param in options_var:
command += ' ---' + param + '=' + str(data[param])
else:
command += ' -' + param + ' ' + str(data[param])
command += utils.parse_fileupload_parameters(data,
fileupload_parameters,
tool, result_dir, ',')
return utils.run_command(command, output_choice, tool, 'tab',
result_dir)
def _run(self, data):
output_choice = 'display'
(boolean_var, fileupload_parameters
) = utils.get_boolean_file_params(service_dir + '/' +
tool.replace('-', '_') + '.yml')
exclude = fileupload_parameters + ['content-type']
for x in fileupload_parameters:
exclude = exclude + [x + '_string', x + '_string_type']
command = utils.perl_scripts + '/' + tool
result_dir = utils.make_tmp_dir(tool)
matrix_title = dict()
matrix_format = dict()
for param in data:
if 'matrix_title_' in param and data[param] != '':
p = re.compile('matrix_title_(\d)')
num = p.search(param)
matrix_title[int(num.group(1)) - 1] = data[param]
elif 'matrix_format_' in param and data[param] != '':
p = re.compile('matrix_format_(\d)')
num = p.search(param)
matrix_format[int(num.group(1)) - 1] = data[param]
elif param == 'o':
command += ' -o ' + result_dir + '/' + data[param]
elif param in boolean_var:
if data[param] == True:
command += ' -' + param
elif data[param] == False:
continue
elif data[param] is not None and data[
param] != '' and param not in exclude:
if 'uth_' in param:
uth_type = param.split('_', 1)
command += ' -uth ' + uth_type[1] + ' ' + str(data[param])
elif 'lth_' in param:
lth_type = param.split('_', 1)
command += ' -lth ' + lth_type[1] + ' ' + str(data[param])
else:
command += ' -' + param + ' ' + str(data[param])
upload_str = utils.parse_fileupload_parameters(data,
fileupload_parameters,
tool, result_dir, ',')
upload_str = re.sub(r"matrix_\d+", "matrix", upload_str)
matrix_file = re.split('\s*-matrix\s*', upload_str)
upload_str = ''
for key in matrix_title:
if matrix_title[key] != '':
upload_str += ' -matrix ' + matrix_title[
key] + ' ' + matrix_file[key +
1] + ' ' + matrix_format[key]
command += upload_str
command += ' -outdir ' + result_dir + ' -prefix ' + tool
return utils.run_command_background(command, tool, result_dir,
data['o'] + '_SUMMARY.html')
def _run(self,data): output_choice = 'display' fileupload_parameters = ['i'] exclude = fileupload_parameters + ['content-type'] for x in fileupload_parameters: exclude = exclude + [x + '_string', x + '_string_type'] command = utils.perl_scripts + '/' + tool result_dir = utils.make_tmp_dir(tool) for param in data: if data[param] is not None and data[param] != '' and param not in exclude: command += ' -' + param + ' ' + str(data[param]) command += utils.parse_fileupload_parameters(data, fileupload_parameters, tool, result_dir, ',') return utils.run_command(command, output_choice, tool, 'fasta', result_dir)
def _run(self,data):
output_choice = 'display'
(boolean_var, fileupload_parameters) = utils.get_boolean_file_params(service_dir+'/' + tool.replace('-','_') +'.yml')
exclude = fileupload_parameters + ['content-type']
for x in fileupload_parameters:
exclude = exclude + [x + '_string', x + '_string_type']
result_dir = utils.make_tmp_dir(tool)
command = utils.perl_scripts + '/' + tool
for param in data:
if param in boolean_var:
if data[param] == True:
command += ' -' + param
elif data[param] == False:
continue
elif data[param] is not None and data[param] != '' and not param in exclude:
command += ' -' + param + ' ' + str(data[param])
command += utils.parse_fileupload_parameters(data, fileupload_parameters, tool, result_dir, ',')
return utils.run_command(command, output_choice, tool, data['out_format'], result_dir)
def _run(self, data):
output_choice = 'display'
(boolean_var, fileupload_parameters
) = utils.get_boolean_file_params(service_dir + '/' +
tool.replace('-', '_') + '.yml')
exclude = fileupload_parameters + ['content-type']
for x in fileupload_parameters:
exclude = exclude + [x + '_string', x + '_string_type']
# background model
exclude += ['markov_order', 'org', 'seq_type', 'seq_type_2']
command = utils.perl_scripts + '/' + tool
result_dir = utils.make_tmp_dir(tool)
for param in data:
if param in boolean_var:
if data[param] == True:
command += ' -' + param
elif data[param] == False:
continue
elif param == 'seq_type' and data[
param] is not None and data[param] != '':
seq_file = utils.parse_fileupload_parameters(
data, ['seq_file'], tool, result_dir, ',')
seq_file_ops = seq_file.strip().split(' ')
command += ' -seq ' + data['seq_type'] + ' ' + seq_file_ops[1]
elif param == 'seq_type_2' and data[
param] is not None and data[param] != '':
seq_file = utils.parse_fileupload_parameters(
data, ['seq_file_2'], tool, result_dir, ',')
seq_file_ops = seq_file.strip().split(' ')
command += ' -seq ' + data['seq_type_2'] + ' ' + seq_file_ops[1]
elif param == 'perm' and data[
param] is not None and data[param] != '':
command += ' -perm ' + data['seq_type'] + ' ' + str(
data[param])
elif param == 'plot' and data[
param] is not None and data[param] != '':
command += ' -plot ' + data['seq_type'] + ' ' + data[param]
elif param == 'perm_2' and data[
param] is not None and data[param] != '':
command += ' -perm ' + data['seq_type_2'] + ' ' + str(
data[param])
elif param == 'plot_2' and data[
param] is not None and data[param] != '':
command += ' -plot ' + data['seq_type_2'] + ' ' + data[param]
elif param == 'org' and data[
param] is not None and data[param] != '':
len = 1
if 'markov_order' in data and data[
'markov_order'] is not None and data[
'markov_order'] != '':
len = data['markov_order'] + 1
command += ' -bgfile ' + utils.get_backgroundfile(
data['org'], len) + '.gz'
elif data[param] is not None and data[
param] != '' and param not in exclude:
command += ' -' + param + ' ' + str(data[param])
command += utils.parse_fileupload_parameters(data,
['m', 'ms', 'bgfile'],
tool, result_dir, ',')
command += ' -o ' + result_dir + '/' + tool
return utils.run_command_background(command, tool, result_dir,
tool + '_synthesis.html')
