ó
ÃKUc           @   s	  d  d l  Z  d  d l Z d  d l Z d  d l Z 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 Z d  d l Z d „  Z d „  Z d „  Z d „  Z d „  Z d „  Z d	 „  Z e d
 „ Z d d „ Z d „  Z i  i  d „ Z d „  Z d „  Z d d „ Z d d d „ Z  d „  Z! d „  Z" d „  Z# d „  Z$ d „  Z% d „  Z& d „  Z' d „  Z( d „  Z) d „  Z* d „  Z+ d „  Z, d „  Z- d  „  Z. d! „  Z/ d" „  Z0 d# „  Z1 d$ „  Z2 d% „  Z3 d& „  Z4 d' „  Z5 d( „  Z6 d) d d* „ Z7 d S(+   iÿÿÿÿN(   t   deepcopyc      	   C   sE  i  } x8| j  ƒ  D]*} |  d k rÜ g  | D]2 } t d | d ƒ D] }	 | | | |	 ^ qC q, | | <| d k r=| | j g  t j | d ƒ D]> \ }
 } t d | d ƒ D] }	 | | |
 | f |	 ^ q® q‘ ƒ q=q |  d k r t t j g  | D]2 } t d | d ƒ D] }	 | | | |	 ^ qqø Œ  ƒ | | <q q W| S(   st   param dict to vector
    Args:
       parammodel,params,sortmarkers:
       width,compcount,order:
    Returns:
    t   parami   i   t   nonparam(   t   keyst   xranget   extendt	   itertoolst   combinationst   listt   chain(   t
   parammodelt   paramst   sortmarkerst   widtht	   compcountt   ordert   paramvect   tpart   markert   windt   mark1t   mark2(    (    s   lib/HistoneUtilities.pyt   paramdict2vec   s    ChYc         C   sU   t  g  |  j ƒ  D]> } |  | j ƒ  D]' } |  | | j ƒ  D] } | ^ q< q$ q ƒ S(   s   returns width of paramdict
    (   t   maxR   (   t	   domparamsR   R   t   curw(    (    s   lib/HistoneUtilities.pyt   getWidth/   s    c         C   s^   d } xQ |  j  ƒ  d j ƒ  D]9 } t | ƒ t k r t | ƒ | k r t | ƒ } q q W| S(   s   returns the order
    i   i    (   t   valuesR   t   typet   tuplet   len(   R   R   t   curkey(    (    s   lib/HistoneUtilities.pyt   getOrder5   s
    $c         C   s^   i  } xQ |  j  ƒ  D]C } |  | GH|  | j  ƒ  GHt d ƒ x |  | j  ƒ  D] } qL Wq Wd S(   sD   shuffles mark data
    Args:
       chro2markinfo:
    Returns:
    i   N(   R   t   exit(   t   chro2markinfot   modchro2markinfot   chrot   mark(    (    s   lib/HistoneUtilities.pyt   genShuffleMarkData>   s    	
c         C   s   d S(   sF   permutes marker data
    Args:
       chro2markinfo:
    Returns:
    N(    (   R"   (    (    s   lib/HistoneUtilities.pyt   genPermuteTestMarkDataM   s    c   "      C   ss  i  } xf|  j  ƒ  D]X\ } } i  } xD | D]< \ } } | j | | d d ƒ | | | d c d 7<q, W| GH| | } t d | d ƒ }	 t j | |	 ƒ }
 t d „  |
 Dƒ ƒ } t | t |	 ƒ Aƒ d k sØ t ‚ t |
 ƒ } g  | D] } t | ƒ ^ që } t	 j
 | ƒ d g } x: t d t | ƒ d ƒ D] } | j | | | | ƒ q3Wt | ƒ d k ru| d } n  |	 d | d !g } x> t t | ƒ d ƒ D]& } | j |	 | | | | d !ƒ q W| j |	 | d | !ƒ g  | D] } t | ƒ d k ré| ^ qé} t d „  | Dƒ ƒ } i  i  } } xK | D]C \ } } | j | | d g  ƒ | | | d j | | f ƒ q7Wx[ | j ƒ  D]M } | j | ƒ s¦q‹n  | | } t	 j
 | ƒ t | d | | !ƒ | | <q‹Wg  | j ƒ  D] } | | D] } | ^ q÷qé} t | ƒ | | <t g  | D] \ } } | | d ^ q&ƒ t g  | D] \ } } | | d ^ qPƒ t g  | D] \ } } | | d ^ qzƒ } } } | | k r½| | k sÃt ‚ t d „  | Dƒ ƒ } g  | D] } | D] } | ^ qêqà} t |	 ƒ }  t d „  | Dƒ ƒ }! t | |  Aƒ d k ret | |! Aƒ d k ret | ƒ t | ƒ k s t ‚ q W| S(   s`   generates shuffled domains
    Args:
       chro2doms,nodemap:
    Returns:
       outdoms:
    i   i    c         s   s"   |  ] } | D] } | Vq q d  S(   N(    (   t   .0t   clut   item(    (    s   lib/HistoneUtilities.pys	   <genexpr>g   s    iÿÿÿÿc         s   s#   |  ] } | d  | d f Vq d S(   i    iÿÿÿÿN(    (   R(   R)   (    (    s   lib/HistoneUtilities.pys	   <genexpr>v   s    c         s   s"   |  ] } | D] } | Vq q d  S(   N(    (   R(   R)   R*   (    (    s   lib/HistoneUtilities.pys	   <genexpr>…   s    c         s   s"   |  ] } | D] } | Vq q d  S(   N(    (   R(   R)   R*   (    (    s   lib/HistoneUtilities.pys	   <genexpr>ˆ   s    (   t   itemst
   setdefaultt   ranget   HistEvalUtilitiest   addEmptyClusterst   setR   t   AssertionErrort   sortedt   randomt   shuffleR   t   appendR   t   has_keyR   t   sum("   t	   chro2domst   nodemapt   outdomsR$   t   domainst   len2distt   startt   endt	   nodecountt   allnodest   truepartt	   seennodest	   trueclustt   clustt   lenst   locst   indt   curclustR)   t   putcurclustt   len2infot   len2domst   mylent   blockst   blockt   putdomst   tsumt   tsum2t   tsum3t   seen1R*   t   tseen1t   seen2t   seen3(    (    s   lib/HistoneUtilities.pyt   genShuffledDomainV   s\    
"	 $+#
0‰&Nc         C   s{  t  |  ƒ } g  }  xbt | ƒ D]T\ } } i  } x,| j ƒ  D]} g  | | <d g t | } x& | | D] \ } } | | | d <qj Wt | ƒ }	 x~ t t | ƒ ƒ D]j }
 t d |
 d ƒ t t | |
 d ƒ } } t	 j
 g  t | | ƒ D] } | | ^ qî ƒ } | |	 |
 <q§ WxD t |	 ƒ D]6 \ } } | d k r"| | j | d | f ƒ q"q"Wq> W|  j t  | ƒ ƒ q W|  S(   sO   smoothing average
    Args:
       marklist:
    Returns:
       marklist:
    g        i   i    i   g•dyáý¥=(   R    t	   enumerateR   t
   nodecountsR   R   R   R   t   mint   npt   meanR5   (   t   marklistt	   tmarklistt   tindt   markinfot   putdictR   t   countvect   post   countt   avgcountvect   ind1t   startindt   endindt   inindt   avgvalt   tval(    (    s   lib/HistoneUtilities.pyt   smoothAverage�   s&    
+/&c      	   C   s  | d k s t  ‚ | r' t |  ƒ }  n  | d k r7 |  St |  ƒ } g  }  | d k rBt | j d	 d
 ƒ ƒ } x¤t | ƒ D]Á \ } } i  } x™ | j ƒ  D]‹ }	 t j g  | |	 D] \ }
 } | ^ q° ƒ t | | ƒ } g  | |	 D]6 \ }
 } t	 j
 j j | | ƒ | k rä |
 d f ^ qä | |	 <q™ W|  j t | ƒ ƒ qz WnÒ| d k rt| d k r`d n d } x«t | ƒ D]ú \ } } i  } xÒ | j ƒ  D]Ä }	 g  | |	 D] \ }
 } | ^ q£} | | t | ƒ k rö| j d g | | t | ƒ ƒ n  t j | ƒ t j | ƒ } } g  | |	 D], \ }
 } | | | | k r |
 d f ^ q | |	 <q’W|  j t | ƒ ƒ qsWn | d k r
x‘t | ƒ D]v \ } } i  } xN | j ƒ  D]@ }	 g  | |	 D]% \ }
 } |
 t j d | ƒ f ^ q½| |	 <q¬W|  j t | ƒ ƒ q�Wn
| d k rt t t d „  | Dƒ ƒ ƒ ƒ } xÙt | ƒ D]¹\ } } t j t | ƒ | | f d t j ƒ} xI t | ƒ D]; \ } }	 x, | |	 D]  \ }
 } | | | |
 d f <q�Wq†Wx¾ t d | | d ƒ D]¥ } t j | d d … | d f ƒ } | d k rÝx4 t | ƒ D]& \ } }	 | | | d f c | :<qWt t | d d … | d f ƒ d ƒ d k  s‚t  ‚ qÝqÝWi  } x\ t | ƒ D]N \ } }	 g  t d | | d ƒ D]  } | | | | d f f ^ q½| |	 <q™W|  j t | ƒ ƒ qEWn | d k rn  |  S(   sy   marker data modifier
    Args:
       marklist,nodecounts:
       prepromodel,avgmode:
    Returns:
       marklist:
    t   binarys	   binary0.5t	   loglineart   lineart   logitt   colnorms   poisson0.99s
   poisson0.9t   poissont    i   g        g      à?g      ð?c         s   s(   |  ] } | j  ƒ  D] } | Vq q d  S(   N(   R   (   R(   R`   R%   (    (    s   lib/HistoneUtilities.pys	   <genexpr>Ó   s    t   dtypeNgü©ñÒMbP?t   stddev(   s   binarys	   binary0.5s	   loglinearRo   Rp   Rq   s   poisson0.99s
   poisson0.9(   s   poisson0.99s
   poisson0.9(   s   binarys	   binary0.5(   R1   Rl   R    t   floatt   replaceRX   R   R[   R7   t   scipyt   statsRr   t   cdfR5   t   dictR   R   R\   t   stdt   matht   logR2   R   R0   t   zerost   float64R   t   abs(   R]   RY   t   prepromodelt   avgmodeR^   t   thresvalt   mindR`   Ra   R   Rc   Rd   t   meanvalt   countst   stdvalR   R   t   valst   tnodet   divsumt   rind(    (    s   lib/HistoneUtilities.pyt   modifyMarkerData¨   sh    :O#%E>"(#=Fgšd~ÅQÊc            sx   t  |  ƒ d k r |  d St |  ƒ ‰ ˆ ˆ  k r6 ˆ  St ‡  ‡ f d †  |  Dƒ ƒ } ˆ | d k rs t j | ƒ n ˆ  S(   sb   log sum of exponentials
    Args:
       xs: list of expo coefs
    Returns:
       sumval:  
    i   i    c         3   s.   |  ]$ } | ˆ  k r t  j | ˆ ƒ Vq d  S(   N(   R}   t   exp(   R(   R*   (   t   NEGINFt   maxval(    s   lib/HistoneUtilities.pys	   <genexpr>ú   s    g        (   R   R   R7   R}   R~   (   t   xsR�   t   sumval(    (   R�   R�   s   lib/HistoneUtilities.pyt	   logSumExpî   s    c   	      C   s,  t  g  |  D] \ } } t | | d ƒ ^ q
 d d „  ƒ} d g  } } xV | D]N } t | ƒ t | ƒ } } | | k r“ | j t | | ƒ ƒ n  | d } qO W| t | ƒ k rÖ | j t | t | ƒ d ƒ ƒ n  g  | D] } t | ƒ d k rÝ | ^ qÝ } g  | D] } | d | d f ^ q} | S(   sh   gets empty clusters
    Args:
       domains,allnodes:
    Returns:
       emptydoms: empty domains
    i   t   keyc         S   s   |  d S(   Ni    (    (   R*   (    (    s   lib/HistoneUtilities.pyt   <lambda>  s    i    iÿÿÿÿ(   R2   R-   RZ   R   R5   R   (	   R;   R@   R=   R>   t   part1t   curint   part2RD   t   part(    (    s   lib/HistoneUtilities.pyt   getEmptyClustersÿ   s    ;#+'c         C   s@   t  |  ƒ } t  | ƒ } t  | ƒ } t  | ƒ } | | | | f S(   se   get cumulative dist
    Args:
       node2start,node2end,node2notstart,node2notend:
    Returns:
    (   t   getCumulative(   t
   node2startt   node2endt   node2notstartt   node2notendt   cumnode2startt   cumnode2endt   cumnode2notstartt   cumnode2notend(    (    s   lib/HistoneUtilities.pyt	   getCumuls  s
    c   
         sÜ   t  ‡  f d †  |  Dƒ ƒ } t j | d | d f d t j ƒ} d „  t | d ƒ Dƒ } xs |  D]k \ } } } t | ˆ  ƒ t | ˆ  ƒ } }	 | | |	 f c | 7<| |	 k rc | |	 | f c | 7<qc qc W| | f S(   s}   makes interaction matrix from raw data
    Args:
       locs:
       resol:
    Returns:
       freqmat:
       in2loc: 
    c         3   s-   |  ]# } | d  d !D] } | ˆ  Vq q d S(   i    i   N(    (   R(   R+   R*   (   t   resol(    s   lib/HistoneUtilities.pys	   <genexpr>*  s    i   Rt   c         S   s#   i  |  ] } | | d  f | “ q S(   i   (    (   R(   RG   (    (    s   lib/HistoneUtilities.pys
   <dictcomp>,  s   	 (   R   R[   R   Rv   R   t   int(
   RF   R¥   t   maxindt   freqmatt   in2loct   pos1t   pos2Rd   Rf   t   ind2(    (   R¥   s   lib/HistoneUtilities.pyt   makeInterMatrix!  s    	&!c         C   s×   i  } |  j  d ƒ r* t j |  d ƒ } n t |  d ƒ } | �’ } xˆ | D]€ } | j ƒ  j d ƒ d d !\ } } } | j d d ƒ } t | ƒ t | ƒ }	 }
 | j | t ƒ  ƒ | | j	 |	 |
 f ƒ qI WWd QX| S(	   sa   reads bed file returns set of regions
    Args:
       fpath:
    Returns:
       chro2vals:
    s   .gzt   rs   	i    i   t   chrRs   N(
   t   endswitht   gzipt   opent   rstript   splitRw   R¦   R,   R0   t   add(   t   fpatht	   chro2valst   opmethodt   infilet   linet   chrostrt   startstrt   endstrR$   R=   R>   (    (    s   lib/HistoneUtilities.pyt   readBedFile5  s    	%!c      
   C   sË  d \ } } } } i  d } } |  j d ƒ rC t j |  d ƒ } n t |  d ƒ } | �m}	 xc|	 D][}
 |
 j ƒ  }
 |
 j d ƒ sb |
 j d ƒ rC| d k s¤ t ‚ d } |
 j ƒ  d d	 !\ } } } | j d
 d ƒ } | d k rö | | k rö qb n  t	 | j d d ƒ ƒ t	 | j d d ƒ ƒ } } d } | j
 | t ƒ  ƒ q½|
 j d ƒ rÀ| d k sdt ‚ d } |
 j ƒ  d } | j d
 d ƒ } | d k rª| | k rªqb n  | j
 | t ƒ  ƒ q½| d k r9| d k rê| | k rêqb n  t	 |
 ƒ d k r,| | j | | | | d t	 |
 ƒ f ƒ n  | d 7} q½| d k r½| d k rc| | k rcqb n  g  |
 j d ƒ D] } t	 | ƒ ^ qs\ } } | d k rº| | j | | f ƒ qºq½qb qb WWd QX| S(   sk   reads wig file, checks extension
    Args:
       fpath:
       sentchro:
    Returns:
       vals:   
    i    s   .gzR®   t   trackt	   fixedStept   variablet   fixedi   iÿÿÿÿs	   chrom=chrRs   s   start=s   step=t   variableStepi   s   	N(   NNNN(   t   NoneR°   R±   R²   R³   t
   startswithR1   R´   Rw   R¦   R,   R0   Rµ   (   R¶   t   sentchroR$   R=   t   stept   outmodeR‰   t   curcountR¸   R¹   Rº   R»   R¼   t   stepstrR*   Rd   (    (    s   lib/HistoneUtilities.pyt   readWigFileK  sP    	10.*c            s  i  } | d k r( d |  d f g } nÖ | d k rd d |  d f d	 |  d
 f d |  d f g } nš | d k rþ g  t  | ƒ D]' } d j | d
 ƒ |  d | f ^ q} g  t  | ƒ D]+ } d j | d
 ƒ |  d | d
 f ^ q´ d |  d | f g } n  | d k rd
 n | ‰ xî | D]æ \ }	 ‰  ‡  ‡ ‡ f d †  t | ƒ Dƒ | |	 <d t | ƒ ˆ ˆ }
 ‰ x– t | |	 j ƒ  ƒ t ˆ  ƒ ˆ ˆ k  r| |	 j ‡  ‡ ‡ ‡ f d †  t t j | |
 ƒ ƒ Dƒ ƒ |
 d
 7}
 ˆ t t	 t j | |
 ƒ ƒ ƒ 7‰ qmWqW| S(   s¹   vec to dict params
    Args:
       sentcoefsm,sortmarkers,width:
       infermodel,classcount: classcount only for crflatent model
       compcount:
    Returns:
       paramdict:
    s   single-memms   single-memm2t   termi    t   crft   semicrft   pseudot   boundt   insidei   t   emptyi   t	   crflatents   bound{0}s	   inside{0}c            s>   i  |  ]4 \ ‰  } ‡  ‡ ‡ ‡ f d  †  t  ˆ ƒ Dƒ | “ q S(   c            sH   i  |  ]> } ˆ ˆ  ˆ ˆ | ˆ ˆ  ˆ ˆ | d  ˆ !| d  “ q S(   i   (    (   R(   R   (   RG   t   solxt
   ucompcountR   (    s   lib/HistoneUtilities.pys
   <dictcomp>�  s   	 (   R   (   R(   R   (   RÔ   RÕ   R   (   RG   s   lib/HistoneUtilities.pys
   <dictcomp>�  s   	 c            sA   i  |  ]7 \ ‰  } ‡  ‡ ‡ ‡ ‡ f d  †  t  ˆ ƒ Dƒ | “ q S(   c            sP   i  |  ]F } ˆ ˆ ˆ  ˆ ˆ | ˆ ˆ ˆ  ˆ ˆ | d  ˆ !| d  “ q S(   i   (    (   R(   R   (   R…   RÔ   t
   startcountRÕ   R   (    s   lib/HistoneUtilities.pys
   <dictcomp>“  s   	 (   R   (   R(   t	   marktuple(   RÔ   RÖ   RÕ   R   (   R…   s   lib/HistoneUtilities.pys
   <dictcomp>“  s   	 (   s   single-memms   single-memm2(   s   crfRÎ   RÏ   N(
   R   t   formatRÄ   RX   R   R   t   updateR   R   R   (   t	   sentcoefsR   R   t
   infermodelt
   classcountR   t	   paramdictt   vallistt   cindt   curpart   curorder(    (   RÔ   RÖ   RÕ   R   s   lib/HistoneUtilities.pyt   sol2dict~  s     	0Ž&-<
*c         C   sZ   d „  |  j  ƒ  Dƒ } x= |  j  ƒ  D]/ } x& |  | D] \ } } | | | | <q4 Wq# W| S(   sY   processes marker data
    Args:
       markinfo:
    Returns:
       mark2pos2count:
    c         S   s   i  |  ] } i  | “ q S(    (    (   R(   R   (    (    s   lib/HistoneUtilities.pys
   <dictcomp>   s   	 (   R   (   R`   t   mark2pos2countR   Rc   Rd   (    (    s   lib/HistoneUtilities.pyt   processMarkData™  s
    c         C   s_   t  d „  |  Dƒ ƒ } t  d „  |  Dƒ ƒ } t  t d | d ƒ ƒ j | | Bƒ } | | | f S(   sr   get locations
    Args:
       sorteddoms:
       nodecount:
    Returns:
       boundlocs,indomlocs,remlocs:
    c         s   s"   |  ] } | D] } | Vq q d  S(   N(    (   R(   t   tdomR_   (    (    s   lib/HistoneUtilities.pys	   <genexpr>¯  s    c         s   s5   |  ]+ \ } } t  | d  | ƒ D] } | Vq  q d S(   i   N(   R   (   R(   R=   R>   R_   (    (    s   lib/HistoneUtilities.pys	   <genexpr>°  s    i   (   R0   R-   t
   difference(   t
   sorteddomsR?   t	   boundlocst	   indomlocst   remlocs(    (    s   lib/HistoneUtilities.pyt   getLocs§  s    &c         C   s‚   t  |  j ƒ  ƒ d k r d St |  j ƒ  ƒ } i d d 6|  d d 6} x5 t d | d ƒ D]  } | | d |  | | | <qZ W| S(   sa   cumulative distribution
    Args:
       node2negprob:
    Returns:
       cumnode2negprob: 
    i    g        i   i   N(   R   R   RÄ   R   R   (   t   node2negprobt   maxnodet   cumnode2negprobt   node(    (    s   lib/HistoneUtilities.pyR›   ¸  s    c      
   C   s¥   g  } x� |  D]‡ } | d k  r9 | j  d g | ƒ q n  | j | ƒ xK t | d ƒ D]9 } | j t j | d d t | d ƒ | d ƒ ƒ qW Wq Wt j | ƒ S(   s[   gets compcount params
    Args:
       retvec,compcount:
    Returns:
       countvec:
    g{®Gáz„?g        i   g      ð?(   R   R5   R   R}   t   powRv   R[   t   array(   t   retvecR   Rb   R*   RG   (    (    s   lib/HistoneUtilities.pyt   getCompParsÇ  s    ;c         C   sˆ  g  | D]S } t  d | d | ƒ D]5 } |  | j | | ƒ rQ |  | | | n d ^ q" q } g  } x¢ t | ƒ D]” \ }	 } | j | d | d |	 | d ƒ x` t  d | ƒ D]O } | j | d | d |	 | d | | d | d |	 | d | ƒ q´ Wqs W| d k r„| g  t j t t | ƒ ƒ d ƒ D]A \ }
 } t  | ƒ D]( } | | |
 | | | | | ^ qOq97} n  | S(   sy   get count vector
    Args:
       mark2pos2count,node:
       sortmarkers,width,order:
    Returns:
       countvec:
    iÿÿÿÿi   g        i   (   R   R6   RX   R5   R   R   R-   R   (   Rã   Rï   R   R   R   R   t   wint   precountvecRb   R…   Rf   R¬   (    (    s   lib/HistoneUtilities.pyt   getCountVecÛ  s    `%Qmc      	   C   sL   t  |  d ƒ �7 } x- | D]% \ } } | j d j | | ƒ ƒ q WWd QXd S(   sd   writes domain file
    Args:
       domoutfile:
       domains:
       comp2scale:
    Returns:
    t   ws   {0},{1}
N(   R²   t   writeRØ   (   t
   domoutfileR;   t   outfileR=   R>   (    (    s   lib/HistoneUtilities.pyt   writeDomainFileî  s    c         C   sû   g  g  g  } } } t  |  d ƒ �¹ } x¯ | D]§ } | j ƒ  } | d k rj | j t | ƒ ƒ g  } q- n  | j d ƒ rŸ | j t | j d ƒ d ƒ ƒ q- n  | j t g  | j d ƒ D] } t | ƒ ^ q¸ ƒ ƒ q- WWd QX| j t | ƒ ƒ | | f S(   sc   reads domain file of list
    Args:
       domfile:
    Returns:
       domainlist,nodecounts:
    R®   Rs   R?   s   	i   t   ,N(   R²   R³   R5   R   RÅ   R¦   R´   R   (   t   domfilet
   domainlistt	   curdomainRY   R¹   Rº   R*   (    (    s   lib/HistoneUtilities.pyt   readMultiDomainFileû  s     ?c      	      sH   t  |  d ƒ �3 } | j d j ‡  f d †  t | ƒ Dƒ ƒ ƒ Wd QXd S(   sˆ   writes domain file of list
    Args:
       domoutfile:
       domainlist: list of domain partition
       nodecounts:
    Returns:
    R÷   s   

c         3   s?   |  ]5 \ } } d  j  ˆ  | ƒ d j d „  | Dƒ ƒ Vq d S(   s   nodecount	{0}
s   
c         s   s'   |  ] \ } } d  j  | | ƒ Vq d S(   s   {0},{1}N(   RØ   (   R(   R=   R>   (    (    s   lib/HistoneUtilities.pys	   <genexpr>  s    N(   RØ   t   join(   R(   RG   t   domain(   RY   (    s   lib/HistoneUtilities.pys	   <genexpr>  s    N(   R²   Rø   R  RX   (   Rù   Rþ   RY   Rú   (    (   RY   s   lib/HistoneUtilities.pyt   writeMultiDomainFile  s    c      
   C   s}   t  | d ƒ �h } x^ |  j ƒ  D]P } | j d j | ƒ ƒ x1 |  | D]% \ } } | j d j | | ƒ ƒ qF Wq WWd QXd S(   s[   write multiscale domain file
    Args:
       scale2dms:
       outfpath:
    Returns:
    R÷   s
   scale	{0}
s   {0},{1}
N(   R²   R   Rø   RØ   (   t
   scale2domst   outfpathRú   t   scaleR=   R>   (    (    s   lib/HistoneUtilities.pyt   writeMultiscaleDomainFile  s
    c      
   C   sµ   i  d } } t |  d ƒ �“ } x‰ | D]� } | j ƒ  } | j d ƒ rm t | j d ƒ d ƒ } g  | | <q& | j d ƒ } | | j t | d ƒ t | d ƒ f ƒ q& WWd QX| S(   s[   reads multiscale domain file
    Args:
       domfile:
    Returns:
       scale2doms:
    R®   R  s   	i   Rü   i    N(   RÄ   R²   R³   RÅ   Rv   R´   R5   R¦   (   Rý   R  t   curscaleR¹   Rº   t   splitted(    (    s   lib/HistoneUtilities.pyt   readMultiscaleDomainFile*  s    5c      
   C   sº   g  g  } } t  |  d ƒ �… } x{ | D]s } | j ƒ  } | d k rc | j t | ƒ ƒ g  } q& n  | j d ƒ } | j t | d ƒ t | d ƒ f ƒ q& WWd QX| j t | ƒ ƒ | S(   sP   reads domain file
    Args:
       domfile:
    Returns:
       domainlist:
    R®   Rs   Rü   i    i   N(   R²   R³   R5   R   R´   R¦   (   Rý   Rþ   t   domsR¹   Rº   R	  (    (    s   lib/HistoneUtilities.pyt   readDomainFile>  s    1c      	   C   sN   t  |  d ƒ �9 } g  | D]% } d „  | j ƒ  j d ƒ Dƒ ^ q } Wd QX| S(   sH   reads pos file
    Args:
       fpath:
    Returns:
       locs:   
    R®   c         s   s   |  ] } t  | ƒ Vq d  S(   N(   Rv   (   R(   R*   (    (    s   lib/HistoneUtilities.pys	   <genexpr>[  s    s   	N(   R²   R³   R´   (   R¶   R¹   Rº   RF   (    (    s   lib/HistoneUtilities.pyt   readPosFileS  s    8c      
   C   sN   t  | d ƒ �9 } | j d j g  |  D] } d j | ƒ ^ q% ƒ ƒ Wd QXd S(   sK   writes position file
    Args:
       locs:
       fpath:
    Returns:
    R÷   s   
s   	N(   R²   Rø   R  (   RF   R¶   Rú   t   loc(    (    s   lib/HistoneUtilities.pyt   writePosFile^  s    c         C   sß   g  i  } } t  |  d ƒ �ª } x  | D]˜ } | j ƒ  } | d k rc | j t | ƒ ƒ i  } q& n  | j d ƒ \ } } } t | ƒ t | ƒ } } | j | t ƒ  ƒ | | j	 | | f ƒ q& WWd QX| j t | ƒ ƒ | S(   sS   reads marker count file
    Args:
       fpath:
    Returns:
       marklist: 
    R®   Rs   s   	N(
   R²   R³   R5   R{   R´   R¦   Rv   R,   R0   Rµ   (   R¶   R]   R`   R¹   Rº   R   Rc   Rd   (    (    s   lib/HistoneUtilities.pyt   readMarkerFilei  s    !c         C   s<   t  | d ƒ �' } | j d j d „  |  Dƒ ƒ ƒ Wd QXd S(   sM   writes marker file
    Args:
       marklist:
       fpath:
    Returns:
    R÷   s   
c         3   s8   |  ]. ‰  d  j  ‡  f d †  ˆ  j ƒ  Dƒ ƒ d  Vq d S(   s   
c         3   s;   |  ]1 } ˆ  | D]  \ } } d  j  | | | ƒ Vq q d S(   s   {0}	{1}	{2}N(   RØ   (   R(   R   Rc   Rd   (   R`   (    s   lib/HistoneUtilities.pys	   <genexpr>ˆ  s    N(   R  R   (   R(   (    (   R`   s   lib/HistoneUtilities.pys	   <genexpr>ˆ  s    N(   R²   Rø   R  (   R]   R¶   Rú   (    (    s   lib/HistoneUtilities.pyt   writeMarkerFile€  s    c      
   C   s›   t  | d ƒ �† } x| |  j ƒ  D]n } t |  | ƒ t k rj d j g  |  | D] } t | ƒ ^ qL ƒ } n
 |  | } | j d j | | ƒ ƒ q WWd QXd S(   sP   writes meta file
    Args:
       metadata:
       objoutfile:
    Returns:
    R÷   s   	s   {0}	{1}
N(   R²   R   R   R   R  t   strRø   RØ   (   t   metadatat
   objoutfileRú   R”   R*   t   keystr(    (    s   lib/HistoneUtilities.pyt   writeMetaFile‹  s    /
c      	   C   s    i  } t  |  d ƒ �… } x{ | D]s } | j ƒ  j d ƒ } t | ƒ d k rg t | d ƒ | | d <q g  | d D] } t | ƒ ^ qr | | d <q WWd QX| S(   sK   read meta file
    Args:
       deconfile:
    Returns:
       metata:
    R®   s   	i   i   i    N(   R²   R³   R´   R   Rv   (   t	   deconfileR  R¹   Rº   R	  R*   (    (    s   lib/HistoneUtilities.pyt   readMetaFileš  s    5c   	      C   s¬  d „  } i  d } } t |  d ƒ ��} xw| D]o} | j ƒ  } t g  d d d d d g D] } | | k rr t n t ^ qZ g  d d	 g D]! } | j | ƒ r£ t n t ^ qˆ ƒ } | rÏ | } i  | | <q/ n  | j d
 ƒ } t | ƒ d k r5| | j	 | d i  ƒ | | d ƒ | | | d t
 | d ƒ <q/ t | ƒ d k r/ | | j	 t | d d !ƒ i  ƒ | | d ƒ | | t | d d !ƒ t
 | d ƒ <q/ q/ WWd QX| S(   sV   read domain param file
    Args:
       parampath:
    Returns:
       paramdict:
    c         S   sE   |  j  d ƒ d k r; g  |  j d ƒ D] } t | ƒ ^ q% St |  ƒ S(   s	   
        Rü   iÿÿÿÿ(   t   findR´   Rv   (   R*   t   tcur(    (    s   lib/HistoneUtilities.pyt   processItem³  s    &R®   R=   R>   RÌ   RÒ   t   interRÐ   RÑ   s   	i   i    iÿÿÿÿi   i   iþÿÿÿN(   RÄ   R²   R³   t   anyt   Truet   FalseRÅ   R´   R   R,   R¦   R   (	   t	   parampathR  RÝ   R   R¹   Rº   R*   t   foundvalR	  (    (    s   lib/HistoneUtilities.pyt   readDomainParamFile¬  s$    	r
-!@c         C   s:   t  |  d ƒ �% } x | D] } t | j ƒ  ƒ SWWd QXd S(   s   
    R®   N(   R²   R¦   R³   (   R¶   R¹   Rº   (    (    s   lib/HistoneUtilities.pyt   readNodecountË  s    c         C   s2   t  |  d ƒ � } | j d j | ƒ ƒ Wd QXd S(   s   
    R÷   s   {0}
N(   R²   Rø   RØ   (   R¶   R?   Rú   (    (    s   lib/HistoneUtilities.pyt   writeNodecountÒ  s    c   	         s‰  t  ‡  f d †  ˆ  j ƒ  Dƒ ƒ } t  ‡  f d †  ˆ  j ƒ  Dƒ ƒ } t |  d ƒ �0} x&ˆ  j ƒ  D]} | j d j | ƒ ƒ | j d j g  | D]U } ˆ  | | j ƒ  D]: } d j | | d j d „  ˆ  | | | Dƒ ƒ ƒ ^ qª q’ ƒ d ƒ | j d	 j g  | D]i } ˆ  | | j ƒ  D]N } d
 j t | ƒ t | ƒ d j d „  ˆ  | | | Dƒ ƒ g ƒ d ^ q qƒ ƒ qc WWd QXd S(   sW   write domain param file
    Args:
       parampath:
       paramdict:
    Returns:
    c         3   s>   |  ]4 } ˆ  | j  ƒ  D] } t | ƒ t k r | Vq q d  S(   N(   R   R   R   (   R(   t	   probparamR   (   RÝ   (    s   lib/HistoneUtilities.pys	   <genexpr>ã  s    c         3   s>   |  ]4 } ˆ  | j  ƒ  D] } t | ƒ t k r | Vq q d  S(   N(   R   R   R   (   R(   R%  R   (   RÝ   (    s   lib/HistoneUtilities.pys	   <genexpr>ä  s    R÷   s   {0}
s   
s   {0}	{1}	{2}Rü   c         s   s   |  ] } t  | ƒ Vq d  S(   N(   R  (   R(   t   citem(    (    s   lib/HistoneUtilities.pys	   <genexpr>ì  s    Rs   s   	c         s   s   |  ] } t  | ƒ Vq d  S(   N(   R  (   R(   R&  (    (    s   lib/HistoneUtilities.pys	   <genexpr>í  s    N(   R0   R   R²   Rø   RØ   R  R   R  (	   R   RÝ   t   singlest   multisRú   t   pparamt   singleR   t   partuple(    (   RÝ   s   lib/HistoneUtilities.pyt   writeDomainParamFileÙ  s    
""vc         C   sŸ  i  i  d	 d	 d	 f \ } } } } } } t |  d ƒ �W} xM| D]E\ } }	 |	 j ƒ  }	 |	 j d ƒ rs d } q@ n  |	 j d ƒ rŽ d } q@ n  | d k r° |	 j d ƒ d } q@ | d k rý g  |	 j d ƒ d D]$ }
 |
 d k rî t |
 ƒ n d	 ^ qÐ } q@ | d k r3|	 j d ƒ } t | d ƒ | | d <q@ | d k r@ |	 j d ƒ } g  | d D] }
 t |
 ƒ ^ qY| t | d d !ƒ <q@ q@ WWd	 QX| | | | f S(
   s€   read hawkes param file
    Args:
       parampath:
    Returns:
       mudict:
       alphadict:
       kerntype,kernmeans:
    R®   t   alphat   mui    s   	i   RÄ   i   N(   RÄ   R²   R³   RÅ   R´   Rv   R   (   R   t   mudictt	   alphadictt   kerntypet	   kernmeanst   mumodet   curmodeR¹   RG   Rº   R*   R	  (    (    s   lib/HistoneUtilities.pyt   readHawkesParamFileð  s*    	'AAt   gaussc   
      C   só   t  |  d ƒ �Þ } | j d j | ƒ ƒ | j d j d j | ƒ ƒ ƒ | j d d j g  | j ƒ  D] } d j | | | ƒ ^ qc ƒ d ƒ | j d d j g  | j ƒ  D]0 \ \ } } }	 d	 j | | d j |	 ƒ ƒ ^ qª ƒ d ƒ Wd
 QXd
 S(   sž   write hawkes param file
    Args:
       parampath:
       mudict:
       alphadict:
       kerntype: kernel type
       kernmeans: if None 
    Returns:
    R÷   s   kerntype	{0}
s   kernmeans	{0}
s   	s   mu
s   
s   {0}	{1}s   alpha
s   {0}	{1}	{2}N(   R²   Rø   RØ   R  R   R+   (
   R   R/  R0  R1  R2  Rú   R   R   R   RÞ   (    (    s   lib/HistoneUtilities.pyt   writeHawkesParamFile  s
    
G(8   t   ost   syst   timet   numpyR[   t   networkxt   nxR±   R   R}   R3   t   copyR    R.   t   scipy.statsRx   R   R   R    R&   R'   RW   Rl   R  R�   R“   Rš   R¤   R­   R¾   RÄ   RË   Râ   Rä   Rë   R›   Ró   Rö   Rû   R   R  R  R
  R  R  R  R  R  R  R  R"  R#  R$  R,  R5  R7  (    (    (    s   lib/HistoneUtilities.pyt   <module>   sb   								7	F			3																						 