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Copy pathconsts.py
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consts.py
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import numpy as np
import logging
#P_DEL = 0.02
P_DEL = 0.02
#P_SUB = 0.022
P_SUB = 0.022
#P_INS = 0.017
P_INS = 0.017
P_COR = 1 - P_DEL - P_SUB - P_INS
Alphabet = "ATGC"
TRACE_NUM = 4
#ORIGINAL = "T"*10
ORIGINAL = "".join(np.random.choice(list(Alphabet), size=100, replace=True))
CUSTOM_TRACES = ["ACCATAATGCGTGGGGCTGACCTCGGAATGCGTGGTCTCCATGCGCGTTTCCTCCAACCTAAGGTAGCCTGTAGTTCATTGACCTCTGATGGCGCTTATAGAAACCGGGAA",
"ACCATAATGCGTGGGGCCGACCTCGGAATGCGGTCTCCATGCGCGTTTCCTCAACCTAAGGTAGCCTGATTCATTGGACCTCTGATGGCGCTTATAGAAACTGGGGAA",
"ACCATAATGCGTGGGGCCGACCTCGGGAATGCGGTCTCCATGCGCGTTTCCTCCAACCTAAGGTAGCCTGTAGTTCATTGGACCTCTGATGGCGCTTATAGAAACCGGGAA",
"ACCATAATGCGTGGGCCGACCTCAGAATGCGGTCTCCATGCGCGTTTCCTCCAACCTAAGGTAGCCTGTAGTTCATTGGACCTCTGATGGCGCTTATAGAAACCGGGAA",
"ACCATAATGCGTGGGGCCGACCTCGGAGATGCGGTCACCATGCGCGTTTCCTCCAACCTAAGGTAGCCTGTAGTTCATTGGACCTCTGATGGCGCTTACTTATAGAAACCGGGA",
"ACCATAATGCGTGGGGCCGACTCCGGAATGCGGTCTCCATGCGCGTTTCTCCAACCTAAGGTAGCCTGTAGTTCATTGACCTCTGATGGCGCTTATGAAACCGGGAA",
"ACCATAATGCGTGGGGCCGACCTTCGGAATGCGGTCTCCATGCGCGTTTCCTCCAACCTAAGGTAGCCTGTAGTTCATTGGACCTCTGATGGCGCTTTATAGAAACCGGGAA",
"ACCATAATGCGTGGGGCCGACCTCCGGAATGCGGTCTCCATACGCGTTTTCCTCCAACCTAAGGTAGCCTGTAGTTCGTGGACCTCTGATGGCGCTTATAGAAACCGGGAGA",
"ACCATAATGCGTGGGGCCAGCCTCGGAATGCGGTCTCCATGCGCGTTCCTCCAACCTAAGGTAGCCACAGTTCATTTGGACCTCTGATGGCCTTATAGAAACCGGGAA",
"ACCATAATGCGTGGGGCCGACCTCGGAAATGCGGTCTCCATGCGCGTTTCCTCCAACCTAAGGTAGCCTTAGGAAGTTCATTGGACTCTGATGGCGCTTATAGAAACCGGGAA",
"ACCATAATGCGTGGGGCCGACCTCGGAATGCGGTCTCCATGCGCGTTTCCTCCAACCTAAGGGTAGCCTGCAGTTCATTGGACCTCTGATGGCGCTTATGGAAACCAGGA",
"ACCATAATGCGTGGGCAACCTCGGAATGCGGTCTCCATGCGCGTTTCCTCCAACCTAAGGTAGCCTGTAGTTCATTGGACCTCTGATGGCGCTTATAGGAAACCGGGAA",
"ACCATAATGCGTGGGGCCGACCTCGGAATGCGGTCTCCATGCGCGTTTCCCTCCAACCTAAAGGTAGCCTGCAGATTTCGTGGACCTCTGATGGCGCTTATAGAAACCGGGAA",
"ACCATAATGCGTGGGGCCGACCTCGGAATGCGGTCTCCATATACGTTTCTCCAACCTAAGGTAGCCTGTAGTTCATTGGACCTCTGATGGCGCTATAGAAACCGGGAA",
"ACCATAATGCGTGGGGCCGACCTCGGAATGCGGTCTCCATGCGCGTTTCCTCCAACCTAAGGTAGCCTGTAGTTCATTGGACCTCTGATGGCGCTTTTATAGAAACCGGGAA"
]
CUSTOM_ORIGINAL = "ACCATAATGCGTGGGGCCGACCTCGGAATGCGGTCTCCATGCGCGTTTCCTCCAACCTAAGGTAGCCTGTAGTTCATTGGACCTCTGATGGCGCTTATAGAAACCGGGAA"
USE_NANOPORE_DATA_FROM_FILE = True
USE_CUSTOM_TRACES = True
USE_LOG_PROB = True
# trellis BMA related
DEFAULT_BETA_B = 0.1
DEFAULT_BETA_I = 0
DEFAULT_BETA_E = 1
# optimization related
ESTIMATE_SECOND_HALF_REVERSED = True
REMOVE_UNNEEDED_TRELLIS_SOURCES = False
LOGGING_LEVEL = logging.INFO