def _start_quast_main(name,
args,
assemblies,
reference_fpath=None,
output_dirpath=None,
exit_on_exception=True,
num_notifications_tuple=None,
is_first_run=None):
args = args[:]
args.extend([asm.fpath for asm in assemblies])
if reference_fpath:
args.append('-R')
args.append(reference_fpath)
if output_dirpath:
args.append('-o')
args.append(output_dirpath)
args.append('--labels')
def quote(line):
if ' ' in line:
line = '"%s"' % line
return line
args.append(quote(', '.join([asm.label for asm in assemblies])))
import quast
reload(quast)
quast.logger.set_up_console_handler(indent_val=1, debug=qconfig.debug)
quast.logger.set_up_metaquast()
logger.info_to_file(
'(logging to ' +
os.path.join(output_dirpath, qconfig.LOGGER_DEFAULT_NAME + '.log)'))
# try:
return_code = quast.main(args)
if num_notifications_tuple:
cur_num_notifications = quast.logger.get_numbers_of_notifications()
num_notifications_tuple = map(
sum, zip(num_notifications_tuple, cur_num_notifications))
if is_first_run:
labels = [
qconfig.assembly_labels_by_fpath[fpath]
for fpath in qconfig.assemblies_fpaths
]
assemblies = [
Assembly(fpath, qconfig.assembly_labels_by_fpath[fpath])
for fpath in qconfig.assemblies_fpaths
]
return return_code, num_notifications_tuple, assemblies, labels
else:
return return_code, num_notifications_tuple
def _start_quast_main(args, assemblies, reference_fpath=None, output_dirpath=None, num_notifications_tuple=None,
labels=None, run_regular_quast=False, is_combined_ref=False, is_parallel_run=False):
args = args[:]
args.extend([asm.fpath for asm in assemblies])
if reference_fpath:
args.append('-R')
args.append(reference_fpath)
if output_dirpath:
args.append('-o')
args.append(output_dirpath)
args.append('--labels')
def quote(line):
if ' ' in line:
line = '"%s"' % line
return line
args.append(quote(', '.join([asm.label for asm in assemblies])))
import quast
try:
import importlib
importlib.reload(quast)
except (ImportError, AttributeError):
reload(quast)
quast.logger.set_up_console_handler(indent_val=1, debug=qconfig.debug)
if not run_regular_quast:
reference_name = os.path.basename(qutils.name_from_fpath(reference_fpath)) if reference_fpath else None
quast.logger.set_up_metaquast(is_parallel_run=is_parallel_run, ref_name=reference_name)
if is_combined_ref:
logger.info_to_file('(logging to ' +
os.path.join(output_dirpath, qconfig.LOGGER_DEFAULT_NAME + '.log)'))
return_code = quast.main(args)
if num_notifications_tuple:
cur_num_notifications = quast.logger.get_numbers_of_notifications()
num_notifications_tuple = list(map(sum, zip(num_notifications_tuple, cur_num_notifications)))
if is_combined_ref:
labels[:] = [qconfig.assembly_labels_by_fpath[fpath] for fpath in qconfig.assemblies_fpaths]
assemblies[:] = [Assembly(fpath, qconfig.assembly_labels_by_fpath[fpath]) for fpath in qconfig.assemblies_fpaths]
return return_code, num_notifications_tuple
def _start_quast_main(args, assemblies, reference_fpath=None, output_dirpath=None,
num_notifications_tuple=None, is_first_run=None, run_regular_quast=False):
args = args[:]
args.extend([asm.fpath for asm in assemblies])
if reference_fpath:
args.append('-R')
args.append(reference_fpath)
if output_dirpath:
args.append('-o')
args.append(output_dirpath)
args.append('--labels')
def quote(line):
if ' ' in line:
line = '"%s"' % line
return line
args.append(quote(', '.join([asm.label for asm in assemblies])))
import quast
try:
import imp
imp.reload(quast)
except:
reload(quast)
quast.logger.set_up_console_handler(indent_val=1, debug=qconfig.debug)
if not run_regular_quast:
quast.logger.set_up_metaquast()
logger.info_to_file('(logging to ' +
os.path.join(output_dirpath,
qconfig.LOGGER_DEFAULT_NAME + '.log)'))
return_code = quast.main(args)
if num_notifications_tuple:
cur_num_notifications = quast.logger.get_numbers_of_notifications()
num_notifications_tuple = list(map(sum, zip(num_notifications_tuple, cur_num_notifications)))
if is_first_run:
labels = [qconfig.assembly_labels_by_fpath[fpath] for fpath in qconfig.assemblies_fpaths]
assemblies = [Assembly(fpath, qconfig.assembly_labels_by_fpath[fpath]) for fpath in qconfig.assemblies_fpaths]
return return_code, num_notifications_tuple, assemblies, labels
else:
return return_code, num_notifications_tuple
def _start_quast_main(
name, args, assemblies, reference_fpath=None,
output_dirpath=None, exit_on_exception=True, num_notifications_tuple=None):
args = args[:]
args.extend([asm.fpath for asm in assemblies])
if reference_fpath:
args.append('-R')
args.append(reference_fpath)
if output_dirpath:
args.append('-o')
args.append(output_dirpath)
args.append('--labels')
def quote(line):
if ' ' in line:
line = '"%s"' % line
return line
args.append(quote(', '.join([asm.label for asm in assemblies])))
import quast
reload(quast)
quast.logger.set_up_console_handler(indent_val=1, debug=qconfig.debug)
logger.info_to_file('(logging to ' +
os.path.join(output_dirpath,
qconfig.LOGGER_DEFAULT_NAME + '.log)'))
# try:
return_code = quast.main(args)
if num_notifications_tuple:
cur_num_notifications = quast.logger.get_numbers_of_notifications()
num_notifications_tuple = map(sum, zip(num_notifications_tuple,cur_num_notifications))
return return_code, num_notifications_tuple
def _start_quast_main(name,
args,
assemblies,
reference_fpath=None,
output_dirpath=None,
exit_on_exception=True):
args = args[:]
args.extend([asm.fpath for asm in assemblies])
if reference_fpath:
args.append('-R')
args.append(reference_fpath)
if output_dirpath:
args.append('-o')
args.append(output_dirpath)
args.append('--labels')
def quote(line):
if ' ' in line:
line = '"%s"' % line
return line
args.append(quote(', '.join([asm.label for asm in assemblies])))
import quast
reload(quast)
quast.logger.set_up_console_handler(debug=not RELEASE_MODE, indent_val=1)
logger.info_to_file(
'(logging to ' +
os.path.join(output_dirpath, qconfig.LOGGER_DEFAULT_NAME + '.log)'))
# try:
return quast.main(args)
fasta_filepath = os.path.join(dirpath, fasta_filename)
if os.path.isfile(
fasta_filepath
) and fasta_filename == project_name + '.fasta':
new_filepath = os.path.join(
tmp_dir_path,
m.group('suffix') + '.fasta')
shutil.copyfile(fasta_filepath, new_filepath)
contigs_filepaths.append(new_filepath)
if len(contigs_filepaths) == 0:
print >> sys.stderr, 'No ' + project_name + '.fasta files in spades_* subdirectories'
else:
# Constructing a new command line arguments array to run quast.py with.
new_args = []
for opt, arg in options:
new_args.extend([opt, arg])
for contig_filepath in contigs_filepaths:
new_args.append(contig_filepath)
quast.main(new_args)
if os.path.isdir(tmp_dir_name):
shutil.rmtree(tmp_dir_name)
if __name__ == '__main__':
main(sys.argv[1:])
if os.path.isdir(dirpath):
m = spades_dir_pattern.match(dirname)
if m:
for fasta_filename in os.listdir(dirpath):
fasta_filepath = os.path.join(dirpath, fasta_filename)
if os.path.isfile(fasta_filepath) and fasta_filename == project_name + '.fasta':
new_filepath = os.path.join(tmp_dir_path, m.group('suffix') + '.fasta')
shutil.copyfile(fasta_filepath, new_filepath)
contigs_filepaths.append(new_filepath)
if len(contigs_filepaths) == 0:
print >>sys.stderr, 'No ' + project_name + '.fasta files in spades_* subdirectories'
else:
# Constructing a new command line arguments array to run quast.py with.
new_args = []
for opt, arg in options:
new_args.extend([opt, arg])
for contig_filepath in contigs_filepaths:
new_args.append(contig_filepath)
quast.main(new_args)
if os.path.isdir(tmp_dir_name):
shutil.rmtree(tmp_dir_name)
if __name__ == '__main__':
main(sys.argv[1:])