def __init__(self, args):
"""Class that handles the sorting of the seqs."""
A = lambda x: args.__dict__[x] if x in args.__dict__ else None
self.sample_name = A('sample_name')
self.input_fasta_path = A('input_fasta')
self.output_db_path = A('output_db_path')
self.run = terminal.Run()
self.progress = terminal.Progress()
self.stats_dict = collections.Counter()
self.extractor = extractor.Extractor()
self.db = None
self.seq_count_dict = {}
def A(param_id):
return D[param_id][0]
def K(param_id, params_dict={}):
kwargs = copy.deepcopy(D[param_id][1])
for key in params_dict:
kwargs[key] = params_dict[key]
return kwargs
import tRNASeqTools.tables as t
import tRNASeqTools.terminal as terminal
run = terminal.Run()
def set_version():
tRNASeqTools_version = 'unknown'
try:
tRNASeqTools_version = pkg_resources.require("tRNASeqTools")[0].version
except:
# maybe anvi'o is not installed but it is being run from the codebase dir?
# some hacky stuff to get version from the setup.py
try:
setup_py_path = os.path.normpath(
os.path.dirname(os.path.abspath(__file__))) + '/../setup.py'
version_string = [
l.strip() for l in open(setup_py_path).readlines()