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g _ Âg _ òÁc C se | | | | k r[ t | | | | | | ƒ | k r[ t | | | | | | ƒ d } 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 i ( t
log_hyper_323t log_getFETprob( t pt Pt nt Nt log_pthresht
log_pvalue( ( sJ /woldlab/castor/home/georgi/programs/meme_4.11.2/scripts/hypergeometric.pyt getLogFETPvalue s 7$c C s | t k r d St | ƒ Sd S( Ng ( t
_log_smallR ( t x( ( sJ /woldlab/castor/home/georgi/programs/meme_4.11.2/scripts/hypergeometric.pyt my_exp0 s c C s4 | | t k r | S| t d t | | ƒ ƒ Sd S( Ni ( t _mm_natsR R ( t logxt logy( ( sJ /woldlab/castor/home/georgi/programs/meme_4.11.2/scripts/hypergeometric.pyt log_sum16 s c C s* | | k r t | | ƒ St | | ƒ Sd S( s. Return the log(x+y) given log(x) and log(y). N( R ( R R ( ( sJ /woldlab/castor/home/georgi/programs/meme_4.11.2/scripts/hypergeometric.pyt log_sum< s
c C sn | t } t | ƒ } t d | | ƒ } | d t d | ƒ 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 à?i ( t _log10R R ( R t prect formatt log10xt et mt str( ( sJ /woldlab/castor/home/georgi/programs/meme_4.11.2/scripts/hypergeometric.pyt sprint_logxD s
gËPÊÿÿï?gÜ1¯ ð?c C sh t t t t f \ } } } } | | | | } | | } | | }
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\ } } } } } |
St | | |
| ƒ } t } t | ƒ } | d } x9 | t | k rt | | ƒ } t | ƒ } | d } qß W| d } | t | k rDt | | ƒ } n
| d } t } t | ƒ } | d } x9 | t | k r¥t | | ƒ } t | ƒ } | d } qmW| d } | t | k rÒt | | ƒ } n
| d } t | | ƒ t | | ƒ k r*| } t d t | ƒ ƒ } t | | ƒ } n+ t d t | ƒ ƒ } t | | ƒ } | } | | | | | 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 ð?( 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_pt it j( ( sJ /woldlab/castor/home/georgi/programs/meme_4.11.2/scripts/hypergeometric.pyR T sX
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c C sQ | d k r d St | ƒ } t j | ƒ r3 t | St | d ƒ } | t | <| S( Ni g g ð?( R t _lnfact_hasht has_keyR7 ( R t keyt result( ( sJ /woldlab/castor/home/georgi/programs/meme_4.11.2/scripts/hypergeometric.pyt lnfact¨ s
c C s" t | ƒ t | ƒ t | | ƒ S( N( R< ( R t k( ( sJ /woldlab/castor/home/georgi/programs/meme_4.11.2/scripts/hypergeometric.pyt lnbicoµ s c C s/ t | | ƒ t | | | | ƒ t | | ƒ S( N( R> ( t n11t n1_t n_1R ( ( sJ /woldlab/castor/home/georgi/programs/meme_4.11.2/scripts/hypergeometric.pyR ¸ s i c C s
| | B| Bd k sÜ | d d k sÓ | t d k rz t t t t t | ƒ t t t | t t t ƒ ƒ a | a t S| t d k rÓ t t t t t | ƒ t t t t t t | ƒ ƒ a | a t Sn | a n | a | a | a | a t t t t t ƒ a t S( Ni i
i ( t _sn11t
_log_sprobR t _sn1_t floatt _sn_1t _snR ( t n11it n1_it n_1it ni( ( sJ /woldlab/castor/home/georgi/programs/meme_4.11.2/scripts/hypergeometric.pyR ¼ s& 99 c C s t | d d d ƒ S( Ni ( R ( R? ( ( sJ /woldlab/castor/home/georgi/programs/meme_4.11.2/scripts/hypergeometric.pyR Ó s c C s\ d t j d } t t j ƒ d k rC t j | IJt j d ƒ n d } x§| t t j ƒ k ròt j | } | d k r— t j | IJt j d ƒ nN| d k rä y t j t j | ƒ } Wqåt j | IJt j d ƒ qåXn| d k r1y t j t j | ƒ } Wqåt j | IJt j d ƒ qåXn´ | d k r~y t j t j | ƒ } Wqåt j | IJt j d ƒ qåXng | d k rËy t j t j | ƒ } Wqåt j | IJt j d ƒ qåXn t j | IJt j d ƒ | d 7} qL Wt | | | | | | ƒ d } t | d d ƒ } t j | I| I| I| I| IJt j d ƒ d S( Ns USAGE:
%s [options]
# positive successes
# positives
# negative successes
# negatives
-h print this usage message
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