def perform_needle_comparison(self, seq_a, seq_b):
protDB = db_handling.ProteinDatabase()
tempfile = MemoryTempfile(preferred_paths=['/mnt/tmp'])
f1 = tempfile.NamedTemporaryFile(delete=False)
f1.write(seq_a[1].encode('utf-8'))
f1.close()
f2 = tempfile.NamedTemporaryFile(delete=False)
f2.write(seq_b[1].encode('utf-8'))
f2.close()
f3 = tempfile.NamedTemporaryFile(delete=False)
subprocess.run([
'needle --asequence ' + f1.name + ' --bsequence ' + f2.name +
' --gapopen 10.0 --gapextend 0.5 --stdout ' + f3.name +
' < enter_param > /dev/null 2>&1'
],
stdout=subprocess.PIPE,
shell=True)
lines = [line.decode('utf-8') for line in f3.readlines()]
f3.close()
values = self.get_values_from_needle_align(lines)
values.insert(0, seq_a[0])
values.insert(0, seq_b[0])
if values[2] == 0 and values[3] == 0 and values[4] == 0 and values[
5] == 0 and values[6] == 0.0:
os.unlink(f1.name)
os.unlink(f2.name)
os.unlink(f3.name)
self.perform_needle_comparison(seq_a, seq_b)
return
protDB.insert_needle_alignment(values)
os.unlink(f1.name)
os.unlink(f2.name)
os.unlink(f3.name)
def example1():
from memory_tempfile import MemoryTempfile
tempfile = MemoryTempfile()
print(tempfile.fallback)
with tempfile.NamedTemporaryFile(suffix='.jpg', delete=False) as td:
print(td.name)
pass
def example2():
# We now do not want to use /dev/shm or /run/shm and no ramfs paths
# If /run/user/{uid} is available, we prefer it to /tmp
# And we want to try /var/run as a last resort
# If all fails, fallback to platform's tmp dir
from memory_tempfile import MemoryTempfile
# By the way, all paths with string {uid} will have it replaced with the user id
tempfile = MemoryTempfile(preferred_paths=['/run/user/{uid}'], remove_paths=['/dev/shm', '/run/shm'],
additional_paths=['/var/run'], filesystem_types=['tmpfs'], fallback=True)
if tempfile.found_mem_tempdir():
print('We could use any of the followig paths: {}'.format(tempfile.get_usable_mem_tempdir_paths()))
print('And we are using now: {}'.format(tempfile.gettempdir()))
with tempfile.NamedTemporaryFile() as ntf:
# use it as usual...
pass
#! /usr/bin/python3
# -*- coding: utf-8 -*-
import dill
import gzip
import os
from memory_tempfile import MemoryTempfile
tempfile = MemoryTempfile()
PATH_ROOT_DIR = os.path.dirname(os.path.abspath(__file__)).replace("\\",
"/") + "/"
f = tempfile.NamedTemporaryFile(prefix="Test", suffix=".txt")
TEMP_DIR = f.name[:f.name.rfind("/")] + "/"
TEMP_DIR_OBJS = TEMP_DIR + f"python_objects/"
if not os.path.exists(TEMP_DIR_OBJS):
os.makedirs(TEMP_DIR_OBJS)
def save_dict_object(d, file_name_prefix):
with gzip.open(TEMP_DIR_OBJS + file_name_prefix + '.pkl.gz', 'wb') as f:
dill.dump(d, f)
def load_dict_object(file_name_prefix):
with gzip.open(TEMP_DIR_OBJS + file_name_prefix + '.pkl.gz', 'rb') as f:
d = dill.load(f)
return d
# We now do not want to use /dev/shm or /run/shm and no ramfs paths
# If /run/user/{uid} is available, we prefer it to /tmp
# And we want to try /var/run as a last resort
# If all fails, fallback to platform's tmp dir
from memory_tempfile import MemoryTempfile
import memory_tempfile
# By the way, all paths with string {uid} will have it replaced with the user id
tempfile = MemoryTempfile(fallback=False)
if tempfile.found_mem_tempdir():
print('We could use any of the followig paths: {}'.format(
tempfile.get_usable_mem_tempdir_paths()))
print('And we are using now: {}'.format(tempfile.gettempdir()))
with tempfile.NamedTemporaryFile() as ntf:
# use it as usual...
pass