def main():
# Check license
license.check_status()
# Setup of argparse for script arguments
class LicenseAction(argparse.Action):
def __call__(self, parser, namespace, values, option_string=None):
print("License status: %s" % license.message())
sys.exit()
parser = argparse.ArgumentParser(
description="Post-processing of 'nanopolish polya' output file with "
"annotation-based data aggregation and downstream analysis.",
prog="pal_aggr.py")
optional = parser._action_groups.pop()
required = parser.add_argument_group('required arguments')
required.add_argument(
"-fl",
type=str,
default=None,
metavar="path_file",
help="text file of sample name and nanopolish polya output paths",
required=True)
optional.add_argument("-t",
type=int,
default=1,
metavar='num_threads',
help='specify number of threads to use, default = 1')
optional.add_argument("-qc_filter",
action='store_true',
help='process only reads with qc_tag = PASS')
optional.add_argument("--silent",
action='store_true',
help='run script without terminal outputs')
optional.add_argument("-l",
"--license",
action=LicenseAction,
metavar="",
nargs=0,
help='show license status and exit')
parser._action_groups.append(optional)
args = parser.parse_args()
# Preparing logging console for __main__
time_stamp = str(datetime.datetime.now())
numeric_level = getattr(logging, 'INFO', None)
logging.basicConfig(filename='npd-rnaseq-tlk.poly_aggr.' +
time_stamp.replace(" ", "_") + '.log',
level=logging.DEBUG,
format='%(asctime)s\t%(name)-12s\t%(message)s',
filemode='w')
logger = logging.getLogger('pal_aggr')
logger.debug('pal_aggr.py version: %s' % version.__version__)
logger.debug('Input command: python pal_aggr.py ' + " ".join(sys.argv))
# Defining Handler to write messages to sys.stdout
if args.silent:
sys.stdout = open(os.devnull, 'w')
console = logging.StreamHandler(sys.stdout)
console.setLevel(numeric_level)
formatter = logging.Formatter('[%(asctime)s] %(message)s',
datefmt='%y-%m-%d %H:%M:%S')
console.setFormatter(formatter)
logging.getLogger('').addHandler(console)
logger.info(
'Begin aggregation of nanopolish polyA data with npd-rnaseq-tlk ver=%s'
% version.__version__)
logger.info('Number of threads: %i' % args.t)
for run in csv.reader(open(args.fl, 'r'), delimiter='\t'):
if run[0][0] == '#':
continue
sample = run[0]
path = run[1]
logger.info('Creating directory for sample: %s' % sample)
if not os.path.isdir(sample):
os.mkdir(sample)
logger.info('Starting run...')
tx_pd, tx_aggr, gn_pd, gn_aggr, annot = license.np_polya_aggr(
path, args.t, args.qc_filter, args.silent)
# Saving results
logger.info('Saving results...')
tx_pd.to_csv(sample + '/' + 'tx_polyA.csv', index=False)
gn_pd.to_csv(sample + '/' + 'gn_polyA.csv', index=False)
# Store data (serialize)
with open(sample + '/' + 'tx.pickle', 'wb') as handle:
pickle.dump(tx_aggr, handle, protocol=pickle.HIGHEST_PROTOCOL)
with open(sample + '/' + 'gn.pickle', 'wb') as handle:
pickle.dump(gn_aggr, handle, protocol=pickle.HIGHEST_PROTOCOL)
with open(sample + '/' + 'annotation.pickle', 'wb') as handle:
pickle.dump(annot, handle, protocol=pickle.HIGHEST_PROTOCOL)
logger.info('All runs are complete!')
# Import modules
import sys
import argparse
import license
if __name__ == '__main__':
# Check license
license.check_status()
# Setup of argparse for script arguments
class licenseAction(argparse.Action):
def __call__(self, parser, namespace, values, option_string=None):
print("License status: %s" % license.message())
sys.exit()
parser = argparse.ArgumentParser(
description="create gff database for exonfeat analysis",
prog="tx_db.py")
optional = parser._action_groups.pop()
required = parser.add_argument_group('required arguments')
required.add_argument("-gff",
type=str,
default=None,
metavar="<gff_file>",
help="specify path to gff file",
required=True)
required.add_argument("-fa",
type=str,
default=None,
metavar="<fasta_file>",
help="specify path to the fasta file",
def main():
# Check license
license.check_status()
# Setup of argparse for script arguments
class LicenseAction(argparse.Action):
def __call__(self, parser, namespace, values, option_string=None):
print("License status: %s" %license.message())
sys.exit()
parser = argparse.ArgumentParser(description="Performs statistical analysis for differential polyA length"
"distributions between multiple conditions at the transcript"
"and gene level.", prog="pal_diff.py")
optional = parser._action_groups.pop()
required = parser.add_mutually_exclusive_group()
required.add_argument("-run", type=str, default=None, metavar="setup_file",
help="path to text file specifying comparisons to perform, refer to wiki for formatting")
required.add_argument("-sf", action='store_true', help='outputs setup_file template')
optional.add_argument("--silent", action='store_true',
help='use with run option, runs script without terminal outputs')
optional.add_argument("-l", "--license", action=LicenseAction, metavar="", nargs=0,
help='show license status and exit')
parser._action_groups.append(optional)
args = parser.parse_args()
if args.sf:
f = csv.writer(open('pal_diff_setup_file.txt', 'w'), delimiter='\t')
f.writerow(['#comparison_name', 'condition_1', 'condition_2', 'test_type', 'read_cutoff', 'fdr_cutoff'])
else:
# Preparing logging console for __main__
time_stamp = str(datetime.datetime.now())
numeric_level = getattr(logging, 'INFO', None)
logging.basicConfig(filename='npd-rnaseq-tlk.poly_diff.' + time_stamp.replace(" ", "_") + '.log',
level=logging.DEBUG,
format='%(asctime)s\t%(name)-12s\t%(message)s',
filemode='w')
logger = logging.getLogger('pal_diff')
logger.debug('pal_diff.py version: %s' % version.__version__)
logger.debug('Input command: python pal_diff.py ' + " ".join(sys.argv))
# Defining Handler to write messages to sys.stdout
if args.silent:
sys.stdout = open(os.devnull, 'w')
console = logging.StreamHandler(sys.stdout)
console.setLevel(numeric_level)
formatter = logging.Formatter('[%(asctime)s] %(message)s', datefmt='%y-%m-%d %H:%M:%S')
console.setFormatter(formatter)
logging.getLogger('').addHandler(console)
logger.info('pal_diff, %s' % version.__version__)
logger.info('Begin differential testing of tx and gene polyA length distributions between conditions...')
# Parse setup file
runs = dict()
with open(args.run, 'r') as setup_file:
read_sf = csv.reader(setup_file, delimiter='\t')
for line in read_sf:
if line[0][0] == '#':
continue
runs[line[0]] = {'cond1': line[1].split(','),
'cond2': line[2].split(','),
'test': line[3],
'read_co': int(line[4]),
'fdr_co': float(line[5])}
# setup and run tests
license.pal_diff_setnrun(runs)