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g _g _i c C sa | | | | k rW t | | | | | | | k rW t | | | | | | } n d } | S( s Return log of hypergeometric pvalue of #pos successes >= p given marginals
p = positive successes
P = positives
n = negative successes
N = negatives
log_pthresh = short-circuit if p will be greater
i ( t
log_hyper_323t log_getFETprob2( t pt Pt nt Nt log_pthresht
log_pvalue( ( sT /oak/stanford/groups/akundaje/marinovg/programs/meme-5.0.5/scripts/hypergeometric.pyt getLogFETPvalue s 7 c C s | t k r d St | Sd S( Ng ( t
_log_smallR ( t x( ( sT /oak/stanford/groups/akundaje/marinovg/programs/meme-5.0.5/scripts/hypergeometric.pyt my_exp2 s c C s4 | | t k r | S| t d t | | Sd S( Ni ( t _mm_natsR R ( t logxt logy( ( sT /oak/stanford/groups/akundaje/marinovg/programs/meme-5.0.5/scripts/hypergeometric.pyt log_sum18 s c C s* | | k r t | | St | | Sd S( s. Return the log(x+y) given log(x) and log(y). N( R ( R R ( ( sT /oak/stanford/groups/akundaje/marinovg/programs/meme-5.0.5/scripts/hypergeometric.pyt log_sum> s
c C sn | t } t | } t d | | } | d t d | d k rZ d } | d 7} n | | | f } | S( s Print x with given format given logx. Handles very large
and small numbers with prec digits after the decimal.
Returns the string to print.i
g ?i ( t _log10R R ( R t prect formatt log10xt et mt str( ( sT /oak/stanford/groups/akundaje/marinovg/programs/meme-5.0.5/scripts/hypergeometric.pyt sprint_logxF s
c C s t | | } | | k r$ | } n | } x t | | d D]m } t | | } t | | | | } | | | } | | k r | }
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S( ss Return log Prob(>= k successes given n draws w/o replacement
from population of size N containing K successes).i ( t lnbicot rangeR R ( R
t KR t kt log_N_choose_nt maxit it log_K_choose_it log_NmK_choose_nmiR R ( ( sT /oak/stanford/groups/akundaje/marinovg/programs/meme-5.0.5/scripts/hypergeometric.pyR Y s "gP?g1 ?c C sh t t t t f \ } } } } | | | | } | | } | | }
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\ } } } } } |
St | | |
| } t } t | } | d } x9 | t | k rt | | } t | } | d } q W| d } | t | k rDt | | } n
| d } t } t | } | d } x9 | t | k rt | | } t | } | d } qmW| d } | t | k rt | | } n
| d } t | | t | | k r*| } t d t | } t | | } n+ t d t | } t | | } | } | | | | | f S( sm Computes Fisher's exact test based on a
null-hypothesis distribution specified by the totals, and
an observed distribution specified by b1 and b2, i.e.
determines the probability of b's outcomes 1 and 2.
Returns an immutable list consisting of the exact
probability, and assorted p-values (sless, sright, sleft,
slarg) based on the density.i i g ?( i i i i i ( t _log_zerot
log_hyper0t log_hypert _log0_99999999R t _log1_00000001t absR R ( t a1t a2t b1t b2t log_slesst
log_srightt log_sleftt
log_slargeR t row1t col1t maxt mint rtt log_probt log_slargt log_pR$ t j( ( sT /oak/stanford/groups/akundaje/marinovg/programs/meme-5.0.5/scripts/hypergeometric.pyt log_getFETprobn sX
c C s d } | d | d } | d | d } | d | d } | d | d } | d
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} | d | d } | d | } | d } t | d | | d t | d S( Ng giE>g @g~\>g @gA~?g @g>@~)@g @gQf@g @g
ta@g @g&Ԏ@g ?g
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?g*hS@g ?g @( R ( t zR ( ( sT /oak/stanford/groups/akundaje/marinovg/programs/meme-5.0.5/scripts/hypergeometric.pyt lngamm s
c C sQ | d k r d St | } t j | r3 t | St | d } | t | <| S( Ni g g ?( R t _lnfact_hasht has_keyR@ ( R t keyt result( ( sT /oak/stanford/groups/akundaje/marinovg/programs/meme-5.0.5/scripts/hypergeometric.pyt lnfact s
c C s" t | t | t | | S( N( RE ( R R! ( ( sT /oak/stanford/groups/akundaje/marinovg/programs/meme-5.0.5/scripts/hypergeometric.pyR s c C s/ t | | t | | | | t | | S( N( R ( t n11t n1_t n_1R ( ( sT /oak/stanford/groups/akundaje/marinovg/programs/meme-5.0.5/scripts/hypergeometric.pyR s i c C s
| | B| Bd k s | d d k s | t d k rz t t t t t | t t t | t t t a | a t S| t d k r t t t t t | t t t t t t | a | a t Sn | a n | a | a | a | a t t t t t a t S( Ni i
i ( t _sn11t
_log_sprobR t _sn1_t floatt _sn_1t _snR ( t n11it n1_it n_1it ni( ( sT /oak/stanford/groups/akundaje/marinovg/programs/meme-5.0.5/scripts/hypergeometric.pyR( s& 99 c C s t | d d d S( Ni ( R( ( RF ( ( sT /oak/stanford/groups/akundaje/marinovg/programs/meme-5.0.5/scripts/hypergeometric.pyR) s c C s\ d t j d } t t j d k rC t j | IJt j d n d } x| t t j k rt j | } | d k r t j | IJt j d nN| d k r y t j t j | } Wqt j | IJt j d qXn| d k r1y t j t j | } Wqt j | IJt j d qXn | d k r~y t j t j | } Wqt j | IJt j d qXng | d k ry t j t j | } Wqt j | IJt j d qXn t j | IJt j d | d 7} qL Wt | | | | | | d } t | d d } t j | I| I| I| I| IJt j d d S( Ns USAGE:
%s [options]
# positive successes
# positives
# negative successes
# negatives
-h print this usage message
i i s -hi i i s %6.3fe%-5.0f(
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