from anvio.tables.geneclusters import TableForGeneClusters
from anvio.tables.views import TablesForViews
__author__ = "Developers of anvi'o (see AUTHORS.txt)"
__copyright__ = "Copyleft 2015-2018, the Meren Lab (http://merenlab.org/)"
__credits__ = []
__license__ = "GPL 3.0"
__version__ = anvio.__version__
__maintainer__ = "A. Murat Eren"
__email__ = "*****@*****.**"
run = terminal.Run()
progress = terminal.Progress()
pp = terminal.pretty_print
aligners = Aligners()
class Pangenome(object):
def __init__(self, args=None, run=run, progress=progress):
self.args = args
self.run = run
self.progress = progress
self.max_num_gene_clusters_for_hierarchical_clustering = constants.max_num_items_for_hierarchical_clustering
A = lambda x: args.__dict__[x] if x in args.__dict__ else None
self.genome_names_to_focus = A('genome_names')
self.genomes_storage_path = A('genomes_storage')
self.genomes = None
self.project_name = A('project_name')
def get_aligner(self, align_with=None):
"""Return an instance of an aligner"""
from anvio.drivers import Aligners
return Aligners().select(align_with)