示例#1
0
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
示例#2
0
    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)},
                    },
            }
示例#3
0
文件: utils.py 项目: paczian/anvio
    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)
示例#4
0
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
示例#5
0
    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
示例#6
0
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
示例#7
0
# -*- 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"
示例#8
0
# -*- 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"