def main():
parser = argparse.ArgumentParser('CRAMtools bam-style-index')
# Logging flags.
parser.add_argument('-d', '--debug',
action = 'store_const',
const = logging.DEBUG,
dest = 'level',
help = 'Enable debug logging.',
)
parser.set_defaults(level = logging.INFO)
# Required flags.
parser.add_argument('-r', '--reference_fasta_path',
required = False,
help = 'Reference fasta path.',
)
parser.add_argument('-b', '--cram_path',
required = False,
action="append",
help = 'Source cram path.',
)
parser.add_argument('-u', '--uuid',
required = True,
help = 'analysis_id string',
)
parser.add_argument('--tool_name',
required = True,
help = 'cramtools'
)
args = parser.parse_args()
tool_name = args.tool_name
uuid = args.uuid
logger = pipe_util.setup_logging(tool_name, args, uuid)
engine = pipe_util.setup_db(uuid)
hostname = os.uname()[1]
logger.info('hostname=%s' % hostname)
if tool_name == 'index':
cram_path = pipe_util.get_param(args, 'cram_path')
reference_fasta_path = pipe_util.get_param(args, 'reference_fasta_path')
index(uuid, cram_path, reference_fasta_path, engine, logger)
else:
sys.exit('No recognized tool was selected')
def remove_chain(self, chain):
chain_idx = tools.index(self.chain_list, chain)
del self.chain_list[chain_idx]
self.number_of_chains -= 1
import pickle
import numpy as np
import nn
import tools as tl
import os
import sys
import pm
import matplotlib.pyplot as plt
# index
index = tl.index('data/mnist/index.npy')
cwd = str(os.getcwd())
os.system('cat ' + str(sys.argv[0]) + ' >> data/mnist/' + str(sys.argv[0]) +
str(index) + '.py')
print('mnist:- index = {}'.format(index))
#loading the MNIST data
test = pickle.load(open('data/mnist/test', 'rb'))
train = pickle.load(open('data/mnist/train', 'rb'))
print('MNIST data loaded')
#reshaping
tni = []
tti = []
ttl = []
tnl = []
for a, b in zip(train[0], test[0]):
a = np.reshape(a, [1, 28, 28])
b = np.reshape(b, [1, 28, 28])
tni.append(a)
tti.append(b)
