comparison ngsutils/support/llh.py @ 2:7a68005de299 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 9a243c616a4a3156347e38fdb5f35863ae5133f9

1:8187a729d9f4

'''
Methods for calculating log-likelihoods for nucleotide frequencies
'''
import math
import collections
from ngsutils.support import memoize

_default_background = {'A': 0.3, 'T': 0.3, 'C': 0.2, 'G': 0.2}

NucleotideLogLikelihood = collections.namedtuple('NucleotideLogLikelihood', 'A C G T pseudo')

@memoize
def pseudo_count(N, bg):
    '''
    >>> pseudo_count(100, _default_background['A'])

    freqT = Tp / Np

    return NucleotideLogLikelihood(math.log(freqA / bg['A']), math.log(freqC / bg['C']), math.log(freqG / bg['G']), math.log(freqT / bg['T']), pseudo)



if __name__ == '__main__':
    import doctest
    doctest.testmod()

2:7a68005de299

'''
Methods for calculating log-likelihoods for nucleotide frequencies
'''
import collections
import math

from ngsutils.support import memoize

_default_background = {'A': 0.3, 'T': 0.3, 'C': 0.2, 'G': 0.2}

NucleotideLogLikelihood = collections.namedtuple('NucleotideLogLikelihood', 'A C G T pseudo')


@memoize
def pseudo_count(N, bg):
    '''
    >>> pseudo_count(100, _default_background['A'])

    freqT = Tp / Np

    return NucleotideLogLikelihood(math.log(freqA / bg['A']), math.log(freqC / bg['C']), math.log(freqG / bg['G']), math.log(freqT / bg['T']), pseudo)


if __name__ == '__main__':
    import doctest
    doctest.testmod()