def create_list_user(self):
lister = Lister(self.list_of_items.copy())
lister.exec_()
self.list_of_items = lister.user_list_list.copy()
self.user_list.clear()
for el in self.list_of_items:
self.user_list.addItem(el)
cost = 0
cost_data = json.loads(open("data/products2.json").read())
for el in self.list_of_items:
cost += cost_data[el]
for el in self.deleted_items:
cost += cost_data[el]
if cost <= 9999:
self.label_2.setText("Итого: {}₽".format(cost))
else:
self.label_2.setText("Итого: 9999₽+".format(cost))
def consumer(input_q):
while True:
item = input_q.get()
hash = Lister.get_hash(item)
# hash = get_hash(item)
print('{} => {}'.format(hash, item))
input_q.task_done()
return None
def __init__(self, m_file='', path='/', genbank_update=False):
self.M_file = m_file
# Always make sure this file name is correct
self.what = Lister('MAFV3.1.csv')
self.GenBank_update = genbank_update
path_list = where.path_list_make(where.VERT_MAM, where.NCBI_DATA)
print('path_list: ', path_list)
if path == '/':
self.path, t = self.db2gbk_mkdir(where.VALLENDER_DATA, path_list,
self.GenBank_update)
else:
self.path = path
print('self.path: ', self.path)
def __init__(self, path='/', fasta_update=False):
self.FASTA_update = fasta_update
# Always make sure this file name is correct
self.what = Lister('MAFV3.1.csv')
self.org_list = self.what.org_list
self.gene_list = self.what.gene_list
if os.path.isdir(where.GB_FASTA + '/Vallender_Data') is False:
os.mkdir(where.GB_FASTA + '/Vallender_Data')
self.feature_list = [
'CDS',
'Protein',
'Misc_Features',
'Other'] # Feature list for directory tree
path_list = where.path_list_make(where.VERT_MAM, where.NCBI_DATA)
print('path_list: ', path_list)
if path == '/':
self.path, t = self.db2fasta_mkdir(
where.GB_FASTA + '/Vallender_Data', path_list, self.FASTA_update)
else:
self.path = path
print('self.path: ', self.path)
import os
from BioSQL import BioSeqDatabase
from dir_mana import dir_mana
from lister import Lister
home = os.getcwd()
project = "GPCR-Orthologs-Project"
user = "******"
where = dir_mana(home, project)
# Use lister() class here so that we can easily access our Master RNA Accession File
what = Lister('MAFV3.1.csv') # Always make sure this file name is correct
# genes = '%s' % genes.r_repr().rstrip('\n')
arg_string1 = 'gene'
db_list = []
for gene in what.master_gene_list:
arg_string1 += (' %s' % gene)
arg_string2 = 'org'
for org in what.org_list:
arg_string2 += (' %s' % org)
for file in os.listdir('/srv/shiny-server/GPCR-Orthologs-Project/CODE/1_Databases/Vallender Data/'):
if '.db' in str(file):
db_list.append(file)
for db_name in db_list:
server = BioSeqDatabase.open_database(driver='sqlite3', db='/srv/shiny-server/GPCR-Orthologs-Project/CODE/1_Databases/Vallender Data/%s' % db_name)
for sub_db_name in server.keys():
db = server[sub_db_name]
Accession = str(what.A_Get1['HTR1A']['Homo_sapiens'])
Accession, Sup, Version = Accession.partition('.')
Accession = Accession.upper()
try:
from dir_mana import dir_mana
from lister import Lister
# Get child process information
comm = MPI.COMM_WORLD
rank = comm.Get_rank()
size = comm.Get_size()
machine = platform.node()
# Initialize project based functions and variables
home = os.getcwd()
project = "GPCR-Orthologs-Project"
user = "******"
where = dir_mana(home, project)
what = Lister('MAFV3.1.csv')
# Initialize the files and variables used to upload the proper database files
log_file = ''
# THe download list contains 8 lists with file names e.g. [[list1], [list2]....[list8]]
temp_file = 'temp_file.txt' # A JSON file (keys: 'logfile'; 'downloadlist', 'db_name', 'key)
# (values: 'file'; list of lists;, 'refseq-release-vertebrate-mammalian', 'vertebrate-mammalian)
temp_file_flag = True
process_number = rank
home = home + '/CODE/1_Databases/NCBI_Data/refseq/release/multiprocessing'
# Try to open the temporary file. The same file is trying to be accessed by 8 different jobs
# TODO-ROB Make 8 different files with 0-7 labeled
while temp_file_flag is True:
try:
with open(home + '/' + temp_file, mode='r',