ó
å[c           @` s   d  d l  m Z m Z m Z m 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 e j e  Z d d d     YZ d S(   i    (   t   absolute_importt   divisiont   print_functiont   unicode_literalsNt   Compact_graph_prunerc           B` s,   e  Z d    Z d   Z d   Z d   Z RS(   c         C` s   d  S(   N(    (   t   self(    (    s   /oak/stanford/groups/akundaje/marinovg/programs/trinityrnaseq-Trinity-v2.8.4/Analysis/SuperTranscripts/pylib/Compact_graph_pruner.pyt   __init__   s    c         C` sk   | j    } xX | D]P } | j   r t | j    | k r t j d j |   | j |  q q Wd  S(   Nu9   Compact_graph_pruner.remove_burrs - pruning burr node: {}(   t   get_all_nodest   is_burrt   lent   get_seqt   loggert   debugt   formatt
   prune_node(   R   t   tgrapht   max_burr_lengtht   nodest   node(    (    s   /oak/stanford/groups/akundaje/marinovg/programs/trinityrnaseq-Trinity-v2.8.4/Analysis/SuperTranscripts/pylib/Compact_graph_pruner.pyt   remove_burrs   s
    $c         C` sd   |  j  | |  } xK | D]C } | j   } x. | D]& } | j | j    | j |  q2 Wq Wd S(   u§  
        bubble structure:

             X1
            /          ---A    B--
            \  /
             X2


        keep X1 or X2, ideally based on which is in a more highly expressed isoform structure.

        A node in a bubble is defined as:
        - has single parent and single child
        - the parents of child(A) and the children of the parent(B) are identical. (simple bubble structure)
        
        N(   t   _get_bubblest   popt   add_transcriptst   get_transcriptsR   (   R   R   t   max_bubble_node_lengtht   bubble_node_listst   bubble_node_listt	   repr_nodet   sister_bubble_node(    (    s   /oak/stanford/groups/akundaje/marinovg/programs/trinityrnaseq-Trinity-v2.8.4/Analysis/SuperTranscripts/pylib/Compact_graph_pruner.pyt   pop_small_bubbles&   s    c         C` s  t  j d  t   } t   } xß| j   D]Ń} | | k rD q, n  t | j    d k rb q, n  t | j    d k r q, n  | j   j   } | j   j   } | j   | j   @} t |  d k  rŅ q, n  t   }	 xu | D]m }
 t |
 j    d k rqā n  t |
 j    d k r$qā n  t |
 j	    | k rBqā n  |	 j
 |
  qā Wt |	  d k  rkq, n  t  j d j | |	 |   t } x# |	 D] } | | k rt } qqW| ræq, n  x. |	 D]& } t | | <t  j d j |   qĘW| j
 |	  q, W| S(   Nu$   Compact_graph_pruner::_get_bubbles()i   i   u   Found bubble: {} -- {} -- {}uG   Compact_graph_pruner::_get_bubbles(): node {} identifed within a bubble(   R   R   t   listt   dictR   R	   t   get_prev_nodest   get_next_nodesR   R
   t   appendR   t   Falset   True(   R   R   R   R   t   node_found_in_bubbleR   t   child_node_At   parent_node_Bt   bubble_nodest   selected_bubble_nodest   bubble_nodet   seen_bubble_node_alreadyt   selected_bubble_node(    (    s   /oak/stanford/groups/akundaje/marinovg/programs/trinityrnaseq-Trinity-v2.8.4/Analysis/SuperTranscripts/pylib/Compact_graph_pruner.pyR   F   sL    			
(   t   __name__t
   __module__R   R   R   R   (    (    (    s   /oak/stanford/groups/akundaje/marinovg/programs/trinityrnaseq-Trinity-v2.8.4/Analysis/SuperTranscripts/pylib/Compact_graph_pruner.pyR      s   			 (    (   t
   __future__R    R   R   R   t   ost   syst   ret   loggingt   TGrapht   TNodet   TGLOBALSt	   getLoggerR-   R   R   (    (    (    s   /oak/stanford/groups/akundaje/marinovg/programs/trinityrnaseq-Trinity-v2.8.4/Analysis/SuperTranscripts/pylib/Compact_graph_pruner.pyt   <module>   s   "$