ó
ƒå˜[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 d  d l Z d  d l m Z d  d l m Z d  d l m Z d  d l Z e j e ƒ Z d Z e d d d „ Z d	 „  Z d
 „  Z d „  Z d „  Z d „  Z d S(   i    (   t   absolute_importt   divisiont   print_functiont   unicode_literalsN(   t   Compact_graph_whole(   t   Compact_graph_partial(   t   Compact_graph_prunergš™™™™™©?i   c   	      C` sÐ  t  j d j |  ƒ ƒ |  j d | ƒ } t j rW | j d ƒ t  j d j | ƒ ƒ n  t ƒ  } | j | ƒ t j r† | j d ƒ n  | j	 | d ƒ t j r¸ | j d j d ƒ ƒ n  t
 ƒ  } | j	 | ƒ t j rý | j d ƒ t  j d	 j | ƒ ƒ n  t ƒ  } | j | | ƒ t j rE| j d
 ƒ t  j d j | ƒ ƒ n  | j | | ƒ t j r„| j d ƒ t  j d j | ƒ ƒ n  | j | ƒ t j rÀ| j d ƒ t  j d j | ƒ ƒ n  t | ƒ } | S(   u›   
    Create a new splice graph based on the node alignment obj.

    Since some nodes may show up as duplicate (repeat) nodes, assign each a unique ID
    u   refine_alignment({})u   ^^SGRAPH2^^u   ladeda.pre.dotu   # pre-refinement tgraph:
{}u   ladeda.linear_compact.doti    u   ladeda.compact.m{}.dotu   ladeda.partial_compaction.dotu@   # post-refinement partial (suffix/prefix adjustments) tgraph:
{}u   ladeda.burr_removal.dotu   # removing burrs tgraph:
{}u   ladeda.bubble_popping.dotu   # bubbles popped tgraph:
{}u   ladeda.final.dotu   # final tgraph:
{}(   t   loggert   debugt   formatt   to_splice_grapht   TGLOBALSt   DEBUGt
   draw_graphR   t   compact_unbranchedt   compact_graphR   R   t   remove_burrst   pop_small_bubblest   splice_graph_to_node_alignment(	   t   node_alignment_objt   reset_node_idst   max_burr_lengtht   max_bubble_pop_lengtht   refined_tgrapht   graph_compactort   partial_graph_compactort   compact_graph_prunert   splice_graph_node_alignment(    (    s„   /oak/stanford/groups/akundaje/marinovg/programs/trinityrnaseq-Trinity-v2.8.4/Analysis/SuperTranscripts/pylib/Splice_model_refiner.pyt   refine_alignment   s@    				
							c         C` si  t  j  j |  j ƒ  ƒ } t j d t | ƒ ƒ t ƒ  } x7 t d t | ƒ ƒ D]  } | | j	 ƒ  } | | | <qN Wt
 ƒ  } t ƒ  } x# | D] } | j | j ƒ  ƒ } q‹ Wt
 | ƒ } xz | D]r } g  | D] } d  ^ qÊ }	 xC | D]; } | | j ƒ  k rã | j	 ƒ  } | | }
 | |	 |
 <qã qã W| j |	 ƒ q½ Wt j |  j ƒ  | | ƒ } t j d t | ƒ ƒ | S(   Nu   Topologically sorted nodes: i    u   Splice graph node_alignment: (   t   Topological_sortt   topologically_sortt   get_all_nodesR   R   t   strt   dictt   ranget   lent
   get_loc_idt   listt   sett   uniont   get_transcriptst   Nonet   appendt   Node_alignmentt   get_gene_id(   t   tgrapht   topologically_sorted_nodest   aligned_loc_id_post   it   loc_idt   new_alignmentst   transcript_idst   nodet   transcript_idt   new_alignmentt   new_idxR   (    (    s„   /oak/stanford/groups/akundaje/marinovg/programs/trinityrnaseq-Trinity-v2.8.4/Analysis/SuperTranscripts/pylib/Splice_model_refiner.pyR   e   s,    			
c         C` s–  |  j  ƒ  } |  j ƒ  } |  j ƒ  } t | ƒ } t ƒ  } x“ t d t | ƒ d ƒ D]x } xo t | d t | ƒ ƒ D]T } t | | | | ƒ r  | j | ƒ qs t | | | | ƒ rs | j | ƒ qs qs WqS W| rt ƒ  } t ƒ  }	 xN t d t | ƒ ƒ D]7 } | | k rý | j	 | | ƒ |	 j	 | | ƒ qý qý Wt
 j
 | | |	 ƒ }
 t | ƒ } t j d j | | | | d ƒ ƒ |
 St j d ƒ |  Sd  S(   Ni    i   u<   Containments found, reporting reduced set {} of {} = {:.2f}%id   u   No containments found(   R,   t   get_transcript_namest   get_aligned_nodesR#   R&   R"   t   a_contains_bt   addR%   R*   R+   R   R   R	   (   t   node_alignmentt   gene_idt   transcript_namest   aligned_nodest    num_transcripts_before_reductiont   containmentsR0   t   jt   adj_transcript_namest   adj_aligned_nodest   adj_splice_graph_node_alignmentt   num_after_reduction(    (    s„   /oak/stanford/groups/akundaje/marinovg/programs/trinityrnaseq-Trinity-v2.8.4/Analysis/SuperTranscripts/pylib/Splice_model_refiner.pyt   remove_redundant_pathsŠ   s4    	  		c         C` sk   d } x7 t  d t |  ƒ ƒ D]  } |  | d  k	 r | } Pq q W| d k  rg t d j t t ƒ ƒ ‚ n  | S(   Niÿÿÿÿi    u7   Error, didn't find first non-none value among {} and {}(   R"   R#   R)   t   RuntimeErrorR	   t   node_list_At   node_list_B(   t	   node_listt	   begin_idxR0   (    (    s„   /oak/stanford/groups/akundaje/marinovg/programs/trinityrnaseq-Trinity-v2.8.4/Analysis/SuperTranscripts/pylib/Splice_model_refiner.pyt   get_first_node_idxµ   s    c         C` sq   d } x= t  t d t |  ƒ ƒ ƒ D]  } |  | d  k	 r" | } Pq" q" W| d k  rm t d j t t ƒ ƒ ‚ n  | S(   Niÿÿÿÿi    u6   Error, didn't find last non-none value among {} and {}(   t   reversedR"   R#   R)   RH   R	   RI   RJ   (   RK   t   end_idxR0   (    (    s„   /oak/stanford/groups/akundaje/marinovg/programs/trinityrnaseq-Trinity-v2.8.4/Analysis/SuperTranscripts/pylib/Splice_model_refiner.pyt   get_end_node_idxÄ   s    "c         C` s†   t  |  ƒ } t |  ƒ } t  | ƒ } t | ƒ } | | k oE | | k sL t Sx3 t | | d ƒ D] } |  | | | k r` t Sq` Wt S(   Ni   (   RM   RP   t   FalseR"   t   True(   RI   RJ   t   A_startt   A_endt   B_startt   B_endR0   (    (    s„   /oak/stanford/groups/akundaje/marinovg/programs/trinityrnaseq-Trinity-v2.8.4/Analysis/SuperTranscripts/pylib/Splice_model_refiner.pyR:   Õ   s    (   t
   __future__R    R   R   R   t   ost   syst   ret   loggingt   TGrapht   TNodeR+   R   R   R   R   R   t	   getLoggert   __name__R   t   MAX_MM_RATERQ   R   R   RG   RM   RP   R:   (    (    (    s„   /oak/stanford/groups/akundaje/marinovg/programs/trinityrnaseq-Trinity-v2.8.4/Analysis/SuperTranscripts/pylib/Splice_model_refiner.pyt   <module>   s&   "$I	%	+		