def initialize_classifier(self):
filesnpaths.is_file_exists(self.classifier_object_path)
try:
if anvio.DEBUG:
classifier_obj = pickle.load(
open(self.classifier_object_path, 'rb'))
else:
with terminal.SuppressAllOutput():
classifier_obj = pickle.load(
open(self.classifier_object_path, 'rb'))
except UnicodeDecodeError:
raise ConfigError(
"Your classifier object is broken. Probably because you generated is using a different verison "
"of anvi'o. Please create a new one from scratch, and you will probably be golden."
)
try:
self.features = classifier_obj['features']
self.classes = classifier_obj['classes']
self.classifier = classifier_obj['classifier']
except:
raise ConfigError(
"RF class does not like the classifier object it was sent for processing :/ Are you sure you "
"generated it the way you were supposed to?")
self.classifier_initialized = True
self.run.info(
'Random Forest Classifier',
"Initialized with %d features grouped into %d classes." %
(len(self.features), len(self.classes)))
import random
import itertools
from collections import Counter
import anvio
import anvio.db as db
import anvio.tables as t
import anvio.dbops as dbops
import anvio.utils as utils
import anvio.terminal as terminal
import anvio.filesnpaths as filesnpaths
from anvio.learning import RF
from anvio.errors import ConfigError, FilesNPathsError
with terminal.SuppressAllOutput():
import anvio.data.hmm as hmm_data
__author__ = "Developers of anvi'o (see AUTHORS.txt)"
__copyright__ = "Copyleft 2015-2019, the Meren Lab (http://merenlab.org/)"
__credits__ = []
__license__ = "GPL 3.0"
__version__ = anvio.__version__
__maintainer__ = "A. Murat Eren"
__email__ = "*****@*****.**"
__status__ = "Development"
class SCGDomainClassifier(object):
"""The base class for training and predicting"""
def __init__(self, args, run=terminal.Run(), progress=terminal.Progress()):
