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"""Options for calculating uncorrected p-values.""" |
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from __future__ import print_function |
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__copyright__ = "Copyright (C) 2016-2018, DV Klopfenstein, H Tang et al., All rights reserved." |
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__author__ = "DV Klopfenstein" |
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import collections as cx |
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import sys |
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class PvalCalcBase(object): |
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"""Base class for initial p-value calculations.""" |
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def __init__(self, name, pval_fnc, log): |
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self.log = log |
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self.name = name |
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self.pval_fnc = pval_fnc |
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def calc_pvalue(self, study_count, study_n, pop_count, pop_n): |
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"""pvalues are calculated in derived classes.""" |
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fnc_call = "calc_pvalue({SCNT}, {STOT}, {PCNT} {PTOT})".format( |
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SCNT=study_count, STOT=study_n, PCNT=pop_count, PTOT=pop_n) |
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raise Exception("NOT IMPLEMENTED: {FNC_CALL} using {FNC}.".format( |
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FNC_CALL=fnc_call, FNC=self.pval_fnc)) |
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class FisherClass(PvalCalcBase): |
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"""From the 'fisher' package, use function, pvalue_population.""" |
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def __init__(self, name, log): |
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import fisher |
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super(FisherClass, self).__init__(name, fisher.pvalue_population, log) |
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def calc_pvalue(self, study_count, study_n, pop_count, pop_n): |
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"""Calculate uncorrected p-values.""" |
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# k, n = study_true, study_tot, |
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# K, N = population_true, population_tot |
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# def pvalue_population(int k, int n, int K, int N): ... |
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return self.pval_fnc(study_count, study_n, pop_count, pop_n).two_tail |
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class FisherScipyStats(PvalCalcBase): |
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"""From the scipy stats package, use function, fisher_exact.""" |
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fmterr = "STUDY={A}/{B} POP={C}/{D} scnt({scnt}) stot({stot}) pcnt({pcnt}) ptot({ptot})" |
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def __init__(self, name, log): |
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from scipy import stats |
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super(FisherScipyStats, self).__init__(name, stats.fisher_exact, log) |
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def calc_pvalue(self, study_count, study_n, pop_count, pop_n): |
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"""Calculate uncorrected p-values.""" |
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# http://docs.scipy.org/doc/scipy-0.17.0/reference/generated/scipy.stats.fisher_exact.html |
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# |
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# Atlantic Indian YES NO |
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# whales 8 2 | 10 whales study_genes 8 scnt 2 | 10 = study_n |
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# sharks 1 5 | 6 sharks not s_genes 1 5 | 6 |
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# -------- ------ -------- ----- |
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# 9 7 16 = pop_n pop_genes 9 pcnt 7 16 = pop_n |
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# |
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# We use the preceeding table to find the p-value for whales/sharks: |
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# |
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# >>> import scipy.stats as stats |
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# >>> oddsratio, pvalue = stats.fisher_exact([[8, 2], [1, 5]]) |
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# a b c d |
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avar = study_count |
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bvar = study_n - study_count |
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cvar = pop_count - study_count |
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dvar = pop_n - pop_count - bvar |
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assert cvar >= 0, self.fmterr.format( |
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A=avar, B=bvar, C=cvar, D=dvar, scnt=study_count, stot=study_n, pcnt=pop_count, ptot=pop_n) |
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# stats.fisher_exact returns oddsratio, pval_uncorrected |
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_, p_uncorrected = self.pval_fnc([[avar, bvar], [cvar, dvar]]) |
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return p_uncorrected |
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class FisherFactory(object): |
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"""Factory for choosing a fisher function.""" |
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options = cx.OrderedDict([ |
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('fisher', FisherClass), |
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('fisher_scipy_stats', FisherScipyStats), |
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]) |
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def __init__(self, **kws): |
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self.log = kws['log'] if 'log' in kws else sys.stdout |
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self.pval_fnc_name = kws["pvalcalc"] if "pvalcalc" in kws else "fisher" |
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self.pval_obj = self._init_pval_obj() |
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def _init_pval_obj(self): |
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"""Returns a Fisher object based on user-input.""" |
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if self.pval_fnc_name in self.options.keys(): |
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try: |
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fisher_obj = self.options[self.pval_fnc_name](self.pval_fnc_name, self.log) |
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except ImportError: |
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print("fisher module not installed. Falling back on scipy.stats.fisher_exact") |
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fisher_obj = self.options['fisher_scipy_stats']('fisher_scipy_stats', self.log) |
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return fisher_obj |
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raise Exception("PVALUE FUNCTION({FNC}) NOT FOUND".format(FNC=self.pval_fnc_name)) |
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def __str__(self): |
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return " ".join(self.options.keys()) |
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# Copyright (C) 2016-2018, DV Klopfenstein, H Tang et al., All rights reserved. |
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tanghaibao /
goatools
