ó
?îec           @   s•   d  Z  d d l m Z d d l m Z m Z d d l Z d d l Z d d l Z d e f d „  ƒ  YZ	 d e f d „  ƒ  YZ
 d	 d
 „ Z d „  Z d S(   s6   
Script to merge nuc positions

@author: Alicia Schep
iÿÿÿÿ(   t   shell_command(   t   Chunkt	   ChunkListNt	   MergedNucc           B   s#   e  Z d  „  Z d „  Z d „  Z RS(   c	   	      C   sL   | |  _  | |  _ | |  _ | |  _ | |  _ | |  _ | |  _ | |  _ d  S(   N(   t   chromt   startt   endt   occt	   occ_lowert	   occ_uppert   readst   source(	   t   selfR   R   R   R   R   R	   R
   R   (    (    s6   /tmp/pip-install-bGcd2k/NucleoATAC/nucleoatac/merge.pyt   __init__   s    							c         C   sL   d j  t t |  j |  j |  j |  j |  j |  j |  j	 |  j
 g ƒ ƒ } | S(   Ns   	(   t   joint   mapt   strR   R   R   R   R   R	   R
   R   (   R   t   out(    (    s6   /tmp/pip-install-bGcd2k/NucleoATAC/nucleoatac/merge.pyt   asBed   s    Hc         C   s   | j  |  j ƒ  d ƒ d S(   s   write bed line for peaks   
N(   t   writeR   (   R   t   handle(    (    s6   /tmp/pip-install-bGcd2k/NucleoATAC/nucleoatac/merge.pyR      s    (   t   __name__t
   __module__R   R   R   (    (    (    s6   /tmp/pip-install-bGcd2k/NucleoATAC/nucleoatac/merge.pyR      s   			t   NucListc           B   s#   e  Z d  „  Z e d d „ ƒ Z RS(   c         G   s   t  j |  | ƒ d  S(   N(   t   listR   (   R   t   args(    (    s6   /tmp/pip-install-bGcd2k/NucleoATAC/nucleoatac/merge.pyR   !   s    i    c         C   s‡  |  d d k r% t  j |  d ƒ } n t |  d ƒ } t ƒ  } x9| D]1} | j d ƒ j d ƒ } t | d ƒ } t | d ƒ } | d k rÑ t | d	 ƒ }	 t | d
 ƒ }
 t | d ƒ } t | d ƒ } ni | d k r.t | d
 ƒ }	 t | d ƒ }
 t | d ƒ } t | d ƒ t | d ƒ } n t d ƒ ‚ |
 | k rD | j t	 | d | | |	 |
 | | | ƒ ƒ qD qD W| j
 ƒ  | S(   s2   Make a list of chunks from a tab-delimited bedfileiýÿÿÿs   .gzt   rs   
s   	i   i   R   i   i   i   i   t   nuci
   i   s   source must be 'occ' or 'nuc'i    (   t   gzipt   openR   t   rstript   splitt   intt   floatt	   Exceptiont   appendR   t   close(   t   bedfileR   t   min_occt   infileR   t   linet   in_lineR   R   R   R   R	   R
   (    (    s6   /tmp/pip-install-bGcd2k/NucleoATAC/nucleoatac/merge.pyt   read#   s.    	!3
(   R   R   R   t   staticmethodR*   (    (    (    s6   /tmp/pip-install-bGcd2k/NucleoATAC/nucleoatac/merge.pyR       s   	ix   c         C   sž  t  ƒ  } d } d } x| t |  ƒ k  r1| t | ƒ k  r1|  | j | | j k  rt | j |  | ƒ | d 7} q |  | j | | j k r¬ | j | | ƒ | d 7} q |  | j | | j | k  rè | j |  | ƒ | d 7} q |  | j | | j | k r$| j | | ƒ | d 7} q | d 7} q Wx1 | t | ƒ k  re| j | | ƒ | d 7} q5Wx1 | t |  ƒ k  r™| j |  | ƒ | d 7} qiW| S(   Ni    i   (   R   t   lenR   R#   R   (   t	   occ_peakst	   nuc_callst   sept   keept   it   j(    (    s6   /tmp/pip-install-bGcd2k/NucleoATAC/nucleoatac/merge.pyt   mergeC   s0    	'c         C   s  |  j  s= d j t j j |  j ƒ j d ƒ d d !ƒ |  _  n  t j |  j	 d |  j
 ƒ } t j |  j d |  j
 ƒ } t | | |  j ƒ } t |  j  d d ƒ } | j | j ƒ  ƒ | j ƒ  t j |  j  d |  j  d d	 t ƒt d
 |  j  d ƒ t j |  j  d d d d	 t ƒd  S(   Nt   .i    iýÿÿÿR   R   s   .nucmap_combined.bedt   ws   .nucmap_combined.bed.gzt   forces   rm t   presett   bed(   R   R   t   ost   patht   basenamet   nucposR   R   R*   t   occpeaksR&   R3   R/   R   R   R   R$   t   pysamt   tabix_compresst   TrueR    t   tabix_index(   R   R   R   t   newR   (    (    s6   /tmp/pip-install-bGcd2k/NucleoATAC/nucleoatac/merge.pyt	   run_merge^   s    	4
$(   t   __doc__t   pyatac.utilsR    t   pyatac.chunkR   R   R   R>   R9   R   R   R3   RC   (    (    (    s6   /tmp/pip-install-bGcd2k/NucleoATAC/nucleoatac/merge.pyt   <module>   s   #