def main():
option = sys.argv
if len(option) == 1:
error(option, 1, 1)
elif len(option) > 2:
data = openfile(option)
data = compile(data)
data = assembly(data)
name = 'a.exe'
option.pop(0)
op = 0
while len(option) > op:
if option[op] in Option:
if op + 1 < len(option):
name = option[op + 1] + '.exe'
op += 1
save(data, name)
else:
data = openfile(option)
data = compile(data)
data = assembly(data)
def test_sample_data(file):
with tempfile.NamedTemporaryFile(suffix='.fasta') as tmp_file:
assembly(
file,
tmp_file.name,
DEFAULT_ALGORITHM,
error_correction=True,
)
indexed_result = sh.bowtie2(
"-a",
"--local",
"--mp 2,2",
"--rdg 10,2",
"--rfg 10,2",
"-f",
"-x ./sample_data/reference/reference",
f"-U {tmp_file.name}",
)
with pysam_sucks(indexed_result) as file:
evaluation_results = evaluate(file)
print(evaluation_results)
assert evaluation_results.overall_score >= 0.01
def setUp(self):
self.assy = assy = assembly.assembly(None)
self.mol = mol = chem.molecule(assy)
self.a = a = chem.Atom("C", chem.V(0.0, 0.0, 0.0), mol)
self.a.set_atomtype("sp3", True)
#!/usr/bin/python
# coding:utf-8
import metaxml
import conf
import os
import sys
import upload
import conf
import lookup
from archive import Item
import archive
import getpass
import assembly
if __name__ == '__main__':
item = Item(conf.iTMSTransporter, conf.distribute_account, conf.distribute_pwd, conf.bundle_short_version_string, conf.bundle_version, conf.project_path, conf.scheme, conf.configuration, conf.provisioning_profile_name, conf.vendor_id)
# 开始打包
archive.archive(item)
# 获取itmsp
lookup.lookup(item)
# 准备上传
assembly.assembly(item)
# 开始上传
upload.upload(item)
import metaxml
import conf
import os
import sys
import upload
import conf
import lookup
from archive import Item
import archive
import getpass
import assembly
if __name__ == '__main__':
item = Item(conf.iTMSTransporter, conf.distribute_account,
conf.distribute_pwd, conf.bundle_short_version_string,
conf.bundle_version, conf.project_path, conf.scheme,
conf.configuration, conf.provisioning_profile_name,
conf.vendor_id)
# 开始打包
archive.archive(item)
# 获取itmsp
lookup.lookup(item)
# 准备上传
assembly.assembly(item)
# 开始上传
upload.upload(item)
from assembly import assembly
# assembly instruction
instruction = [
' lw 0 1 five load reg1 with 5 (uses symbolic address)',
' lw 1 2 3 load reg2 with -1 (uses numeric address)',
'start add 1 2 1 decrement reg1',
' beq 0 1 2 goto end of program when reg1==0',
' beq 0 0 start go back to the beginning of the loop', ' noop',
'done halt end of program', 'five .fill 5', 'neg1 .fill -1',
'stAddr .fill start'
]
# main
for x in instruction:
assembly(x)
from assembly import assembly, DEFAULT_ALGORITHM
SAMPLE_FILES = [
f'./sample_data/reads_{sample_file}_percent_bad.fasta'
for sample_file in ['1', '1_to_3', '3_to_5']
]
if __name__ == '__main__':
for sample_file in SAMPLE_FILES:
output_file_name = sample_file.split('.')[-2].split('/')[-1]
assembly(
input_file_name=sample_file,
output_file_name=f'./sample_data/output_{output_file_name}.fasta',
algorithm=DEFAULT_ALGORITHM,
error_correction=True,
)
def fem(le, beta_values, num_elements_in_region, total_num_elements, EpsilonR,
MuR):
A, B = assembly(num_elements_in_region, total_num_elements, le,
beta_values, EpsilonR, MuR)
eig_values, eig_vectors = solver(A, B)
return eig_values, eig_vectors