ó
Ý1`Zc           @   s“   d  d l  Z  d  d l m Z d  d l m Z d  d l Z d  d l Z d  d l Z d  d l m Z d  d l	 m
 Z
 d  d l Z d d d „  ƒ  YZ d S(	   iÿÿÿÿN(   t   array(   t   stats(   t   clock(   t
   itemgettert   ReadContainerc           B   s§   e  Z d  „  Z d „  Z e d d „ Z d „  Z d „  Z d „  Z	 d „  Z
 d „  Z d „  Z d	 „  Z d
 „  Z d „  Z d „  Z d „  Z d „  Z d „  Z d „  Z RS(   c         C   sC   i  |  _  i  |  _ i  |  _ i  |  _ i  |  _ d |  _ d |  _ d  S(   Ni    (   t   readst   allreadst   umist	   umi_histot   coveredt   read_numbert   rejected(   t   self(    (    sM   /oak/stanford/groups/akundaje/marinovg/programs/PeakXus/src/ReadContainer6.pyt   __init__   s    						c         C   s8   d } x+ |  j  D]  } | t j |  j  | ƒ 7} q W| S(   Ng        (   R   t   npt   sum(   R   t   ct   key(    (    sM   /oak/stanford/groups/akundaje/marinovg/programs/PeakXus/src/ReadContainer6.pyt   getComplexity*   s     c         C   sH  t  | ƒ } |  j d 7_ | |  j k r: d |  j | <n |  j | c d 7<| |  j k rBi  |  j | <| d  k r‘ | d k r‘ i  |  j | <n  i  |  j | <t d g  ƒ |  j | d <t d g  ƒ |  j | d <| d  k r| d k rt d g  ƒ |  j | d <n  | d  k r<| d k r<t d g  ƒ |  j | d <n  t ƒ  |  j | d <t ƒ  |  j | d <|  j | | j	 t  | ƒ ƒ |  j | | j
 | ƒ | d  k rÍ| d k rÍ|  j | | j
 | ƒ n  | d  k r5i  |  j | <i  |  j | d <i  |  j | d <t ƒ  |  j | | | <|  j | | | j	 | ƒ q5nó| d  k ru| d k ru|  j | | j
 | ƒ n  t |  j | | ƒ d k  r|  j | | j
 | ƒ |  j | | j	 t  | ƒ ƒ | d  k r5t ƒ  |  j | | | <|  j | | | j	 | ƒ q5n'| d  k rM|  j | | j
 | ƒ |  j | | j	 | ƒ nè | |  j | | k rË|  j | | j
 | ƒ |  j | | j	 | ƒ t ƒ  |  j | | | <|  j | | | j	 | ƒ nj | |  j | | | k r5|  j | | j
 | ƒ |  j | | j	 | ƒ |  j | | | j	 | ƒ n  |  j d 7_ d  S(   Ni   t   it   +t   -g      ð?(   t   intR   R   R   t   NoneR   R	   R    t   sett   addt   appendR   t   lenR
   (   R   t   chromt   strandt	   fiveprimeR   t   save_umit   umi(    (    sM   /oak/stanford/groups/akundaje/marinovg/programs/PeakXus/src/ReadContainer6.pyt   addRead/   sb         " "c      	   C   s  t  } t  } | d  k rs t ƒ  }	 t | d ƒ > }
 t j |
 d d ƒ} x | D] } |	 j | d ƒ qO WWd  QXn  | j d ƒ d } | d k r§ t j	 | d ƒ } n t j	 | d ƒ } | j
 | ƒ } xI| D]A} | j rä qÏ n  | j | j ƒ } d	 } | j rd
 } n  | d  k r•g  t | j ƒ D]+ \ } } | d j d ƒ d k r*| ^ q*} | j | d d |  } | j ƒ  } | |	 k r›qÏ q›n d  } | d	 k r¾| j | j d } n	 | j } | d k  rÙqÏ n  | d	 k rît } n t } |  j | | | | | | ƒ qÏ W| o| S(   Nt   rbt	   delimiters   	i    t   .iÿÿÿÿt   samt   rR   R   t   BCi   (   t   FalseR   R   t   opent   csvt   readerR   t   splitt   pysamt   Samfilet   fetcht   is_unmappedt   getrnamet   rnamet
   is_reverset	   enumeratet   tagst   countt   uppert   aendt   rlent   TrueR!   (   R   t   pathR   t   outdirt   umilenR   t	   ref_chromt   hasReadsPlust   hasReadsMinust   ref_umist   csvfileR&   t   linet   extt   samfilet   itert   readR   R   R   t   vt   indexR    R   (    (    sM   /oak/stanford/groups/akundaje/marinovg/programs/PeakXus/src/ReadContainer6.pyt   readSamy   sJ    	  	 	 	A 	 	  	 c   	      C   sD  | | k r| t  t j |  j | d | k ƒ d ƒ } t  t j |  j | d | k ƒ d ƒ } | d k rt | | S| | St j | | ƒ } t j | | ƒ } d } x} t | | ƒ D]l } t  t j |  j | d | k ƒ d ƒ | | <t  t j |  j | d | k ƒ d ƒ | | <| d 7} q¸ W| d k r<| | S| | S(   NR   i    R   i   (   R   R   t   whereR   t   zerost   range(	   R   R   t   startt   endt
   count_typet   c_post   c_negRI   R   (    (    sM   /oak/stanford/groups/akundaje/marinovg/programs/PeakXus/src/ReadContainer6.pyt	   getCounts«   s     ** .. c          C   sD  t  t k r| t t j t j t d t  k ƒ d ƒ }  t t j t j t d t  k ƒ d ƒ } t d k rt |  | S|  | St j	 t t  ƒ }  t j	 t t  ƒ } d } x} t
 t  t ƒ D]l } t t j t j t d | k ƒ d ƒ |  | <t t j t j t d | k ƒ d ƒ | | <| d 7} q¸ Wt d k r<|  | S|  | S(   NR   i    R   i   (   RN   RO   R   R   RK   R   R   R   RP   RL   RM   (   RQ   RR   RI   R   (    (    sM   /oak/stanford/groups/akundaje/marinovg/programs/PeakXus/src/ReadContainer6.pyt   getAllCountsÄ   s     ** .. c         C   st   xm |  j  j ƒ  D]\ } t j t |  j  | d ƒ ƒ |  j  | d <t j t |  j  | d ƒ ƒ |  j  | d <q Wd  S(   NR   R   (   R   t   keysR   R    t   sorted(   R   R   (    (    sM   /oak/stanford/groups/akundaje/marinovg/programs/PeakXus/src/ReadContainer6.pyt	   sortReadsÝ   s    +c         C   s¤   t  |  j | d ƒ d k rœ t  |  j | d ƒ d k rœ t |  j | d d |  j | d d g ƒ d t |  j | d d |  j | d d g ƒ f Sd Sd  S(   NR   i    R   iÿÿÿÿi   (   i    i    (   R   R   t   maxt   min(   R   R   (    (    sM   /oak/stanford/groups/akundaje/marinovg/programs/PeakXus/src/ReadContainer6.pyt   getChromSizeæ   s    :bc         C   s7   d } x* |  j  j ƒ  D] } | |  j | ƒ 7} q W| S(   Ni    (   R   RU   RZ   (   R   t   genome_sizeR   (    (    sM   /oak/stanford/groups/akundaje/marinovg/programs/PeakXus/src/ReadContainer6.pyt   getGenomeSizeí   s     c         C   s©   | d  k rY t |  j | d ƒ } t |  j | d ƒ } | j | ƒ } t t | ƒ ƒ S| |  j k r€ t j |  j | | ƒ St j	 j
 d | d ƒ t j d ƒ d  S(   NR   R   s   Chromosome s    not found from data!
i   (   R   R   R   t   unionRV   t   listR   R    t   syst   stderrt   writet   exit(   R   R   R   t   pt   nt   u(    (    sM   /oak/stanford/groups/akundaje/marinovg/programs/PeakXus/src/ReadContainer6.pyt   getReadsô   s     c   	      C   s  |  j  | ƒ \ } } | d k s9 | d k s9 | d k rœ t j |  j | d d | ƒ} | d k r‰ t j | t j | ƒ d d ƒ} n  | d k rœ | Sn  t j |  j | d d | ƒ} | d k rì t j | t j | ƒ d d ƒ} n  | d k r | | S| d k r| S| | S(	   Ns   ++R   R   t	   minlengthi   t   modet   sames   --(   RZ   R   t   bincountR   t   convolvet   ones(	   R   R   t	   hist_typet   st   nproct   NRd   t   h_post   h_neg(    (    sM   /oak/stanford/groups/akundaje/marinovg/programs/PeakXus/src/ReadContainer6.pyt   getReadHisto  s    $  $   $  c   
      C   sÏ   |  j  | | | | ƒ } | GHt | ƒ GHt j | ƒ GHt | d ƒ „ } t j | d d ƒ} | j d d d d d g ƒ xI t d	 t	 | ƒ ƒ D]2 }	 | j | |	 d
 |	 d
 |	 d
 | |	 g ƒ q WWd  QXt
 S(   Nt   wbR#   s   	t
   chromosomeRN   RO   t   idR6   i    i   (   Rs   RX   R   t   argmaxR)   R*   t   writert   writerowRM   R   R:   (
   R   R   Rm   Rn   Ro   t   filenamet   histoRB   t   wR   (    (    sM   /oak/stanford/groups/akundaje/marinovg/programs/PeakXus/src/ReadContainer6.pyt   saveReadHisto  s    6c   	      C   sI  t  |  j j ƒ  ƒ d k  r1 |  j | | | | ƒ S|  j | ƒ \ } } | d k sj | d k sj | d k rÍ t j |  j | d d | ƒ} | d k rº t j | t j | ƒ d d ƒ} n  | d k rÍ | Sn  t j |  j | d d | ƒ} | d k rt j | t j | ƒ d d ƒ} n  | d k r1| | S| d k rA| S| | S(	   Ni   s   ++R   R   Rg   Rh   Ri   s   --(	   R   R   RU   Rs   RZ   R   Rj   Rk   Rl   (	   R   R   Rm   Rn   Ro   Rp   Rd   Rq   Rr   (    (    sM   /oak/stanford/groups/akundaje/marinovg/programs/PeakXus/src/ReadContainer6.pyt   getAllReadHisto&  s"     $  $   $  c         C   s   |  j  S(   N(   R
   (   R   (    (    sM   /oak/stanford/groups/akundaje/marinovg/programs/PeakXus/src/ReadContainer6.pyt   getReadCount<  s    c         C   s   t  |  j j ƒ  ƒ S(   N(   RV   R   RU   (   R   (    (    sM   /oak/stanford/groups/akundaje/marinovg/programs/PeakXus/src/ReadContainer6.pyt   getChromNamesA  s    c         C   s;   t  |  j j ƒ  ƒ d k r d  St j |  j | | ƒ Sd  S(   Ni    (   R   R   RU   R   R   R    (   R   R   R   (    (    sM   /oak/stanford/groups/akundaje/marinovg/programs/PeakXus/src/ReadContainer6.pyt   getUmisF  s     c         C   s   t  t | ƒ ƒ } d } t  t | ƒ ƒ | } t g  | D] } | | | | ^ q8 ƒ } d t j j | | | ƒ } t j | ƒ r‰ d S| S(   Ng      ð?i   (   t   floatR   R   R   t   chi2t   cdft   matht   isnan(   R   t   dataRp   t   mt   theta_0t   yt   chi2_mint   P(    (    sM   /oak/stanford/groups/akundaje/marinovg/programs/PeakXus/src/ReadContainer6.pyt   zeroOrderLeastSquaresJ  s    +N(   t   __name__t
   __module__R   R   R(   R   R!   RJ   RS   RT   RW   RZ   R\   Rf   Rs   R}   R~   R   R€   R   R   (    (    (    sM   /oak/stanford/groups/akundaje/marinovg/programs/PeakXus/src/ReadContainer6.pyR      s"   		J	2													(    (   R*   R    t   scipyR   R_   R-   R…   t   timeR   t   operatorR   t   numpyR   R   (    (    (    sM   /oak/stanford/groups/akundaje/marinovg/programs/PeakXus/src/ReadContainer6.pyt   <module>   s   