def __init__(self,
project=None,
project_path=os.getcwd(),
genbank=GenBank,
**kwargs):
"""Initialize the MultipleSequenceAlignment class.
:param project: The project name.
:param project_path: The path to the project.
:param genbank: The composer parameter which is used to configure the
GenBank class with the MSA class.
:param kwargs: The kwargs are used with the dispatcher as a way to
control the alignment pipeline.
:returns: If the kwargs are utilized with YAML or other
configurations, then this class returns an alignment
dictionary, which can be parsed to run specific alignment algorithms.
"""
self.dispatcher_options = {
"Guidance_config": ["GUIDANCE2", self.guidance2],
"Pal2Nal_config": ["PAL2NAL", self.pal2nal],
"ClustalO_config": ["CLUSTALO", self.clustalo]
}
# Set up loggers
__log = LogIt()
__logfile = None
self.guidancelog = __log.default('guidance2', __logfile)
self.pal2nallog = __log.default('pal2nal', __logfile)
self.clustalolog = __log.default('clustalo', __logfile)
# stop_codons = ['TAG', 'TAA', 'TGA']
self.program = None
self.alignment_dict = {}
self.project = project
self.project_path = project_path
if project_path and project:
self.project_path = Path(project_path) / Path(project)
# Configuration of class attributes
add_self = attribute_config(self,
composer=genbank,
checker=GenBank,
project=project,
project_path=project_path)
for var, attr in add_self.__dict__.items():
setattr(self, var, attr)
# Determine which alignment to configure
# And then run that alignment with the configuration.
for config in self.dispatcher_options.keys():
if config in kwargs.keys():
program = self.dispatcher_options[config][0]
aligner = self.dispatcher_options[config][1]
aligner_configuration = kwargs[config]
self.alignment_dict[program] = [aligner, aligner_configuration]
def test_logit(self):
"""Test the LogIt class."""
logit = LogIt()
test = logit.default(logname='testlog', logfile=self.logfile)
self.assertEqual(str(test.name), 'TESTLOG')
self.assertTrue(os.path.isfile(self.logfile))
logit.shutdown()
logit.deletelog(self.logfile)