ó
'}Lc           @   s•   d  d l  Z  d  d l Z d  d l Z d  d l Z d  d l Z d  d l m Z d  d l m Z e	 Z
 d f  d „  ƒ  YZ e d k r‘ e  j d IJn  d S(   iÿÿÿÿN(   t   poisson_cdf(   t   poisson_cdf_invt
   PeakFinderc           B   s‰   e  Z d  „  Z d „  Z d „  Z d „  Z d „  Z d „  Z d „  Z d „  Z	 d „  Z
 d	 „  Z d
 „  Z d d „ Z d „  Z d „  Z RS(   c         C   s  t  | ƒ d k s$ t  | ƒ d k r3 t d ƒ ‚ n  | |  _ | |  _ d |  _ | d j ƒ  j ƒ  d |  _ d |  _ | d d k r‘ d | d <n  t	 | d ƒ |  _
 | d d k rÁ d | d <n  t | d ƒ |  _ | d d k rñ d	 | d <n  t	 d
 t j t | d ƒ ƒ ƒ d |  _ | d d k r8d | d <n  t	 | d ƒ |  _ | d d k rhd | d <n  t | d ƒ |  _ | d d k r˜d | d <n  t	 | d ƒ |  _ | d d k rÈd | d <n  t	 | d ƒ |  _ | d d k rød | d <n  t	 | d ƒ |  _ | d d k r4|  j d d ƒ | d <n  t	 | d ƒ |  _ | d d k rdd | d <n  t	 | d ƒ |  _ | d d k r”d | d <n  t	 | d ƒ |  _ | d d k rÄd | d <n  t | d ƒ |  _ | d d k rôd | d <n  t	 | d ƒ |  _ d  S(    Ni    s   Empty NEW or POSITIONg    £ááAt   INTERVALt    i
   t
   GENOME_LENt   PVALUEgñhãˆµøä>iœÿÿÿg      $@t	   EXTENSIONiK   t   TAG_NUMg    E,¦At	   MIN_WIDTHiP   t	   MAX_WIDTHiú   t
   MAX_HEIGHTi'  t
   MIN_HEIGHTt   pValg-Cëâ6?t   LOGiÿÿÿÿt   SLOPEt   PEAK_INFLECTION_RATIOg333333ó?t	   MED_WSIZEi   (   t   lent
   ValueErrort   newt   post	   genomeLent   stript   splitt   chrt   pct   intt   intervalt   floatt   matht   log10t
   pvalCutOfft   tagLent   tagNumt   minWidt   maxWidt	   maxHeightt   calcLowerCutOfft	   minHeightt   LoGt   slopet   peak2inflectiont   medWsize(   t   selfR   R   t   par(    (    sC   /woldlab/castor/data00/home/georgi/programs/NPS-1.3.2/PeakFinder.pyt   __init__   s\    $				*c         C   sr   g  } | | d } xW t  | d | d d ƒ D]9 } | j | | | d t j | | d | ƒ ƒ q1 W| S(   Ng      ð?i   i   g       @(   t   ranget   appendR   t   exp(   R,   t   sigmat   maskt   sigma2t   x(    (    sC   /woldlab/castor/data00/home/georgi/programs/NPS-1.3.2/PeakFinder.pyR   h   s
    #7c         C   s   d d d g } | S(   Ni   iþÿÿÿ(    (   R,   t   LapOp(    (    sC   /woldlab/castor/data00/home/georgi/programs/NPS-1.3.2/PeakFinder.pyt   Laplaces   s    c         C   s   d d d g } | S(   Ng      à?g        g      à¿(    (   R,   t   GradOp(    (    sC   /woldlab/castor/data00/home/georgi/programs/NPS-1.3.2/PeakFinder.pyt   Gradient}   s    c         C   sj   g  } | | d } xO t  | d | d d ƒ D]1 } | j d | t j | | d | ƒ ƒ q1 W| S(   Ng      ð?i   i   g       @(   R/   R0   R   R1   (   R,   R2   R3   R4   R5   (    (    sC   /woldlab/castor/data00/home/georgi/programs/NPS-1.3.2/PeakFinder.pyt
   GaussSlope†   s
    #/c         C   sd   | } | j  ƒ  t | ƒ } | d d k rR | | d d | | d d } n | | d } | S(   Ni   i    i   g       @(   t   sortR   (   R,   t   datat   tempt   dataLent   med(    (    sC   /woldlab/castor/data00/home/georgi/programs/NPS-1.3.2/PeakFinder.pyt   median”   s    
%c         C   s   | d k ry t  | ƒ } |  j | | d ƒ } g  } x> t d | ƒ D]- } |  j | | | | !ƒ } | j | ƒ qD W| S| Sd  S(   Ni    i   (   R   t   padDatat   xrangeR@   R0   (   R,   t   seqt   wsizet   seqLent   paddedt   newseqt   it   s(    (    sC   /woldlab/castor/data00/home/georgi/programs/NPS-1.3.2/PeakFinder.pyt	   medFilter¤   s    c   	      C   sq   g  } t  | ƒ } xX t | ƒ D]J } d } x. t | ƒ D]  } | | | | | | 7} q8 W| j | ƒ q W| S(   Ng        (   R   RB   R0   (	   R,   t   arraylenRF   t   filterR=   t   LR5   t   newvaluet   y(    (    sC   /woldlab/castor/data00/home/georgi/programs/NPS-1.3.2/PeakFinder.pyt   convolve¼   s    c         C   sP   g  } g  t  | ƒ D] } d ^ q } | j | ƒ | j | ƒ | j | ƒ | S(   Ni    (   R/   t   extend(   R,   t   arrayt   padlent   newdataR5   t   PAD(    (    sC   /woldlab/castor/data00/home/georgi/programs/NPS-1.3.2/PeakFinder.pyRA   Ê   s    c         C   sP   | d k r! | d | d } n+ | d k  rB | | d d } n
 | | } | S(   Ni    gš™™™™™¹?(    (   R,   t   peakt   trought   peak2trough(    (    sC   /woldlab/castor/data00/home/georgi/programs/NPS-1.3.2/PeakFinder.pyt   getRatioÕ   s    
c         C   sŠ  | d } | d } | | d } |  j  |  j } d | |  j |  j } |  j | } t d | | d ƒ }	 t t | ƒ d | | d ƒ }
 t |	 | | d | ƒ } x3 t d t | ƒ ƒ D] } d | | | | | <qÀ Wt | d | | d |
 d d ƒ } x3 t d t | ƒ ƒ D] } d | | | | | <qWg  } | | k r©t j	 d |  j | ƒ | j
 | |
 |	 d d  ƒ | j
 | d |
 |	 d d ƒ |
 |	 d t | ƒ } | d k  rd | } | d } | | } d g | | |	 |
 d !d g | } | } ng | d k r<| |	 |
 d !} | } nA | d } | | } | |	 |
 d !} d g | | d g | } t t d „  | | ƒ ƒ } d | | } n„ d g |
 |	 d t | ƒ t | ƒ } | j
 | ƒ | j
 | ƒ | j
 | ƒ t t d „  | | |	 |
 d !ƒ ƒ } d | | } t t | d	 ƒ | d
 t ƒ} | d k r`d } n t d t j | ƒ ƒ d } | | | f S(   Ni    i   g      ð?i   iÿÿÿÿsU   Peak width, %d bp is recommended to be larger than tag extension (EXTENSION in *.par)c         S   s   |  | S(   N(    (   R5   RO   (    (    sC   /woldlab/castor/data00/home/georgi/programs/NPS-1.3.2/PeakFinder.pyt   <lambda>  s    c         S   s   |  | S(   N(    (   R5   RO   (    (    sC   /woldlab/castor/data00/home/georgi/programs/NPS-1.3.2/PeakFinder.pyRZ     s    i   t   lowerg        g     d©@iœÿÿÿg      $@(   R!   R   R   R"   t   maxt   minR   R/   t   warningst   warnRQ   t   sumt   mapt   pcdft   roundt   FalseR   R   R   (   R,   t   ratiost   peakLoct   leftt   rightt   widtht   lt   pt   LAMBDAt   startt   endt   weightLRH   t   weightRt   weightt   difft   lpt   rpt   rt   wt   tagCountt   weightMR   (    (    sC   /woldlab/castor/data00/home/georgi/programs/NPS-1.3.2/PeakFinder.pyt   CalcPvalã   s\    

!&!


'		

)&	g-Cëâ6?c         C   s2   d |  j  |  j |  j } t d | | d d ƒS(   Ng      ð?i   t   maximumiè  (   R"   R!   R   t   pcdfi(   R,   R   Rl   (    (    sC   /woldlab/castor/data00/home/georgi/programs/NPS-1.3.2/PeakFinder.pyR&   E  s    c   )      C   s‡  g  } d } t  | ƒ } t } d } d t | ƒ } | d d k  rS d } t } n  d } xG| | k  r¢| rk| | d k rkt } | } | d } | d } t | | ƒ t | | ƒ k  rÇ | } n  t | | ƒ t | | ƒ k  rð | } n  | | k s\ | | d k rq\ n  g  } x, t | | d ƒ D] } | j | | ƒ q,W| j ƒ  t | | ƒ | } t | | | d | d !ƒ | } t | | | | !ƒ | } |  j	 | | ƒ } t
 | | ƒ } t | | ƒ } | | d } |  j	 | | ƒ } | | k  s\ | | k s\ | |	 k  rq\ n  | } | }  | | d }! | |  d }" g  }# x, t | |  d ƒ D] } |# j | | ƒ q`W| |# j t |# ƒ ƒ | d }$ ~# |" |! d }% |% | k rb|% | k rb|  j | | |  g ƒ \ }& }' }( |& |
 k rbt r'| j d |  j |! |" |  j |& |' |( f ƒ n& | j d |  j |! |" |  j |& f ƒ |  j d 7_ qbn  |  } n* | r•| | d k  r•| d } t } n  | d 7} q\ W| rƒ| | d d k  rƒ| d } | d } | } t | | ƒ t | | ƒ k  r | } n  | | d | | d d | k rƒg  } x, t | | d ƒ D] } | j | | ƒ q>W| j ƒ  d } t | | ƒ t | ƒ } t | | | d | d !ƒ | } t | | | | !ƒ | } | | d } |  j	 | | ƒ } t
 | | ƒ } t | | ƒ } | } | }  | | d }! | |  d }" g  }# x, t | |  d ƒ D] } |# j | | ƒ qBW| |# j t |# ƒ ƒ | d }$ ~# |" |! d }% |% | k r€|% | k r€|  j	 | | ƒ } | | k r}| | k r}| |	 k r}|  j | | |  g ƒ \ }& }' }( |& |
 k rzt r?| j d |  j |! |" |  j |& |' |( f ƒ n& | j d |  j |! |" |  j |& f ƒ |  j d 7_ qzq}q€qƒn  | S(   Ni   i   g      ð?i    i   s   %s	%d	%d	%d	%e	%f	%fs   %s	%d	%d	%d	%e(   R   Rd   R   t   Truet   absR/   R0   R;   R`   RY   R]   R\   RB   t   indexRy   t   DEBUGR   R   ()   R,   t   subseqRe   t   logseqt   slopeseqt   minFoldChanget   maxFoldChangeR#   R$   t   minPeak2Inflectiont
   pvalCutofft
   candidatest	   backtrackt   LENGTHt   FOUNDRM   t   overLRm   R5   Rn   t	   boundary1t	   boundary2R=   RV   t   inflectionLt   inflectionRt   inflectionRatiot   inflectionMint   inflectionMaxt
   inflectionR*   t   LEDGEt   REDGEt   LEFTPOSt   RIGHTPOSt   tmpt   PEAKPOSt   WIDTHt   pvalRl   t   tc(    (    sC   /woldlab/castor/data00/home/georgi/programs/NPS-1.3.2/PeakFinder.pyt   strictCandidatesR  sÂ    	

 	 	
#$ !!/&	
	

 	$
#!$!/&c   ,      C   s„  g  } xw|  j  D]l} | j ƒ  j ƒ  } g  t d t | d ƒ t | d ƒ d ƒ D]@ } t | d ƒ | |  j |  j t | d ƒ d | g ^ qT } |  j d k r¾ |  j |  j ƒ } n |  j	 ƒ  } t
 | ƒ d d } |  j d k rú|  j d ƒ } |  j d ƒ }	 |  j d ƒ }
 |  j d ƒ } |  j d ƒ } |  j d ƒ } |  j d k r|  j |  j ƒ } t
 | ƒ d d } n  t
 | ƒ d d } t
 |	 ƒ d d } t
 |
 ƒ d d } t
 | ƒ d d } t
 | ƒ d d } t
 | ƒ d d } n  |  j ƒ  } t
 | ƒ d d } t
 | ƒ } d g | } d g | } |  j d k r¿d g | } d g | } d g | } d g | } d g | } d g | }  |  j d k rÌd g | }! qÌn d g | }" x, t t
 | ƒ ƒ D] }# | |# d | |# <qßW|  j | | ƒ }$ |  j | |$ | ƒ } |  j d k r¬|  j | |  j ƒ } |  j | | ƒ }% |  j | |% | ƒ }  |  j | | |  | |  j |  j |  j |  j |  j |  j ƒ
 }& nÃ|  j d k r6|  j | |  j ƒ } |  j | | ƒ }' |  j | |' | ƒ } |  j | | | | |  j |  j |  j |  j |  j |  j ƒ
 }& n9|  j d k rÀ|  j | |  j ƒ } |  j | | ƒ }( |  j | |( | ƒ } |  j | | | | |  j |  j |  j |  j |  j |  j ƒ
 }& n¯|  j d k rJ|  j | |  j ƒ } |  j | | ƒ }) |  j | |) |
 ƒ } |  j | | | | |  j |  j |  j |  j |  j |  j ƒ
 }& n%|  j d k rÔ|  j | |  j ƒ } |  j | | ƒ }* |  j | |* |	 ƒ } |  j | | | | |  j |  j |  j |  j |  j |  j ƒ
 }& n›|  j d k r^|  j | |  j ƒ } |  j | | ƒ }+ |  j | |+ | ƒ } |  j | | | | |  j |  j |  j |  j |  j |  j ƒ
 }& n|  j d k rè|  j | |  j ƒ } |  j | | ƒ }$ |  j | |$ | ƒ }! |  j | | |! | |  j |  j |  j |  j |  j |  j ƒ
 }& n‡ |  j d k ro|  j | t ƒ } |  j | | ƒ }$ |  j | |$ | ƒ }" |  j | | |" | |  j |  j |  j |  j |  j |  j ƒ
 }& n  | j |& ƒ q W| S(	   Ni    i   i   i   iÿÿÿÿi   i   i   (   R   R   R   RB   R   R   R   R)   R:   R9   R   R(   R   R7   R/   RA   RP   RJ   R+   R   R'   R%   R#   R$   R*   R    RQ   (,   R,   t   peakListt   plnRk   t   jR€   R)   t   L2St   log1t   log2t   log3t   log4t   log5t   log6t	   logCustomt   LCustomt   L1t   L2t   L3t   L4t   L5t   L6t   laplacet   LLRK   Re   t   Slopet   LoG1t   LoG2t   LoG3t   LoG4t   LoG5t   LoG6t	   LoGCustomR7   R5   RF   t   padded6R‡   t   padded5t   padded4t   padded3t   padded2t   padded1(    (    sC   /woldlab/castor/data00/home/georgi/programs/NPS-1.3.2/PeakFinder.pyt	   findPeaksá  sº    r--------(   t   __name__t
   __module__R.   R   R7   R9   R:   R@   RJ   RP   RA   RY   Ry   R&   R   RÀ   (    (    (    sC   /woldlab/castor/data00/home/georgi/programs/NPS-1.3.2/PeakFinder.pyR      s   	W		
									b	t   __main__s/   Use this by importing it in another python file(   t   sysR   t   operatorR^   t   ProbR    Rb   R   R{   Rd   R   R   RÁ   t   stderr(    (    (    sC   /woldlab/castor/data00/home/georgi/programs/NPS-1.3.2/PeakFinder.pyt   <module>   s   0ÿ ÿ S