def gen_output_directory(output_directory,
progress=Progress(verbose=False),
run=Run(),
delete_if_exists=False):
if os.path.exists(output_directory) and delete_if_exists:
try:
run.warning(
'filesnpaths::gen_output_directory: the client asked the existing directory \
"%s" to be removed.. Just so you know :/ (You have 5 seconds to press\
CTRL + C).' % output_directory)
time.sleep(5)
shutil.rmtree(output_directory)
except:
progress.end()
raise FilesNPathsError, "I was instructed to remove this directory, but I failed: '%s' :/" % output_directory
if not os.path.exists(output_directory):
try:
os.makedirs(output_directory)
except:
progress.end()
raise FilesNPathsError, "Output directory does not exist (attempt to create one failed as well): '%s'" % \
(output_directory)
if not os.access(output_directory, os.W_OK):
progress.end()
raise FilesNPathsError, "You do not have write permission for the output directory: '%s'" % output_directory
return output_directory
def __init__(self, from_address='admin@localhost', server_address='localhost', server_port=25,
init_tls=False, username = None, password = None, run = Run(verbose = False),
progress = Progress(verbose=False)):
self.from_address = from_address
self.server_address = server_address
self.server_port = server_port
self.init_tls = init_tls
self.username = username
self.password = password
self.server = None
self.config_ini_path = None
self.run = run
self.progress = progress
self.config_template = {
'SMTP': {
'from_address' : {'mandatory': True, 'test': lambda x: str(x)},
'server_address' : {'mandatory': True, 'test': lambda x: str(x)},
'server_port' : {'mandatory': True, 'test': lambda x: RepresentsInt(x) and int(x) > 0, 'required': 'an integer'},
'init_tls' : {'mandatory': True, 'test': lambda x: x in ['True', 'False'], 'required': 'True or False'},
'username' : {'mandatory': True, 'test': lambda x: str(x)},
'password' : {'mandatory': True, 'test': lambda x: str(x)},
},
}
def run_processes(self, processes_to_run,
progress=Progress(verbose=False)):
tot_num_processes = len(processes_to_run)
sent_to_run = 0
while 1:
NumRunningProceses = lambda: len(
[p for p in self.processes if p.is_alive()])
if NumRunningProceses() < self.num_thread and processes_to_run:
for i in range(0, self.num_thread - NumRunningProceses()):
if len(processes_to_run):
sent_to_run += 1
self.run(processes_to_run.pop())
if not NumRunningProceses() and not processes_to_run:
# let the blastn program finish writing all output files.
# FIXME: this is ridiculous. find a better solution.
time.sleep(1)
break
progress.update('%d of %d done in %d threads (currently running processes: %d)'\
% (sent_to_run - NumRunningProceses(),
tot_num_processes,
self.num_thread,
NumRunningProceses()))
time.sleep(1)
def gen_output_directory(output_directory, progress=Progress(verbose=False), run=Run(), delete_if_exists=False, dont_warn=False):
if not output_directory:
raise FilesNPathsError("Someone called `gen_output_directory` function without an output\
directory name :( An embarrassing moment for everyone involved.")
if os.path.exists(output_directory) and delete_if_exists and not is_dir_empty(output_directory):
try:
if not dont_warn:
run.warning('The existing directory "%s" is about to be removed... (You have \
20 seconds to press CTRL + C). [filesnpaths::gen_output_directory]' % output_directory,
header = '!!! READ THIS NOW !!!')
time.sleep(20)
shutil.rmtree(output_directory)
except:
progress.end()
raise FilesNPathsError("I was instructed to remove this directory, but I failed: '%s' :/" % output_directory)
if not os.path.exists(output_directory):
try:
os.makedirs(output_directory)
except:
progress.end()
raise FilesNPathsError("Output directory does not exist (attempt to create one failed as well): '%s'" % \
(output_directory))
if not os.access(output_directory, os.W_OK):
progress.end()
raise FilesNPathsError("You do not have write permission for the output directory: '%s'" % output_directory)
return output_directory
def __init__(self,
search_path='.',
max_files_and_dirs_to_process=50000,
depth=3,
run=Run(),
progress=Progress()):
self.run = run
self.progress = progress
self.depth = int(depth)
self.search_path = search_path
self.max_files_and_dirs_to_process = max_files_and_dirs_to_process
self.anvio_dbs = {}
for db_path, level in self.walk():
db_info = DBInfo(db_path, dont_raise=True)
if db_info is not None:
if db_info.db_type not in self.anvio_dbs:
self.anvio_dbs[db_info.db_type] = []
# Add a cheeky `level` attribute to db_info for no other reason than to order dbs after the walk
db_info.level = level
self.anvio_dbs[db_info.db_type].append(db_info)
# sort by level, so we know what is closest to the search_path root directory
for db_type in self.anvio_dbs:
self.anvio_dbs[db_type] = sorted(self.anvio_dbs[db_type],
key=lambda d: d.level)
self.anvio_dbs_found = True
def is_file_exists(file_path, dont_raise=False):
if not file_path:
raise FilesNPathsError("No input file is declared...")
if not os.path.exists(os.path.abspath(file_path)):
if dont_raise:
return False
else:
Progress().reset()
raise FilesNPathsError("No such file: '%s' :/" % file_path)
return True
# -*- coding: utf-8
"""Classes and functions for handling, storing, and retrieving atomic data from contigs and splits"""
import anvio
from anvio.sequence import Coverage
from anvio.terminal import Run, Progress
from anvio.terminal import pretty_print as pp
from anvio.variability import VariablityTestFactory
import anvio.tables as t
run = Run()
progress = Progress()
progress.verbose = False
try:
from anvio.columnprofile import ColumnProfile
except ImportError:
run.info_single('C extension for ColumnProfile failed to load, falling back to the Python implementation...', mc = 'gray', nl_after = 1)
from anvio.variability import ColumnProfile
__author__ = "A. Murat Eren"
__copyright__ = "Copyright 2015, The anvio Project"
__credits__ = ["Faruk Uzun"]
__license__ = "GPL 3.0"
__version__ = anvio.__version__
__maintainer__ = "A. Murat Eren"
__email__ = "*****@*****.**"
__status__ = "Development"
# -*- coding: utf-8
"""Classes and functions for handling, storing, and retrieving atomic data from contigs and splits"""
import anvio
from anvio.sequence import Coverage
from anvio.terminal import Run, Progress
from anvio.terminal import pretty_print as pp
from anvio.variability import VariablityTestFactory
import anvio.tables as t
run = Run()
progress = Progress()
progress.verbose = False
try:
from anvio.columnprofile import ColumnProfile
except ImportError:
run.info_single(
'C extension for ColumnProfile failed to load, falling back to the Python implementation...',
mc='gray',
nl_after=1)
from anvio.variability import ColumnProfile
__author__ = "A. Murat Eren"
__copyright__ = "Copyright 2015, The anvio Project"
__credits__ = ["Faruk Uzun"]
__license__ = "GPL 3.0"
__version__ = anvio.__version__
__maintainer__ = "A. Murat Eren"