Python get_default_options Examples

Example #1

File: test_data_subsequence.py Project: JohnReid/STEME

 def setUp(self):
     self.options = stempy.get_default_options()

Example #2

File: find_best_wmers.py Project: JohnReid/STEME

#
# Set up the logging
#
import logging, os, sys, time
from cookbook.script_basics import setup_logging
setup_logging(__file__, level=logging.INFO)
import stempy


def get_fasta_file(filename):
    return os.path.join(os.path.dirname(__file__), '..', 'fasta', filename)

seed = 'TTTAAAATACTTTAAA'
num_to_find = 10000

options = stempy.get_default_options()
options.max_num_sites = options.min_num_sites = 10
options.min_w = options.max_w = W = len(seed)

#
# read in data
#
if 1 < len(sys.argv):
    fasta_file = sys.argv[1]
else:
    fasta_file = os.path.normpath(get_fasta_file('T00759-small.fa'))
algorithm = stempy.Algorithm(options)
algorithm.initialise(fasta_file.encode(sys.stdin.encoding or 'ascii'))
algorithm._initialise_p_value_tables()
data = algorithm.data

Example #3

File: test_find_best_w_mers.py Project: JohnReid/STEME

 def setUp(self):
     self.options = stempy.get_default_options()
     self.options.output_dir = os.path.join('output', 'test-find-best-w-mers')
     self.options.bg_model_order = 0