ó
MÌ¼]c           @   s   d  „  Z  d S(   c      	   C   s¿  d d l  m } m } m } m } m } m }	 m }
 g  } g  } g  } g  } xm |  D]e } | j ƒ  } xP | d t	 | ƒ !D]; } d | k ry t
 | j d ƒ d ƒ } | j | ƒ qy qy WqS W|  j d t t |  | ƒ ƒ j ƒ | j ƒ  | d t
 | ƒ } xy t |  | ƒ D]h \ } } | j ƒ  } | d j d	 ƒ d } | d
 } t t	 | ƒ ƒ } | | k rgPn  | j | ƒ qWy= | | ƒ } |	 | ƒ } d j | | ƒ ƒ j d d ƒ } Wn d } d } n X| d t | ƒ } t | ƒ t | ƒ k  rd t | ƒ | } n  | d t | ƒ k r;d t | ƒ | } n  d t t	 |  ƒ ƒ d t t	 | ƒ ƒ d t | d ƒ } d j | d | | | ƒ j d d ƒ d j | ƒ | | | | g ƒ d S(   Niÿÿÿÿ(   t   taxidlist2LCAt   find_parentst   get_rankt   find_rankofparentst   name1t   find_familyt   id_from_namei   s   NM:t   :i   t   keyi    t   |i	   t    t   _t   NOMATCH_TAXID_NOT_FOUNDt   FAMILY_NOT_FOUNDt   NOMATCH_length_below_i   t   NOMATCH_similarity_below_s   tothits:s   _accepted-hits:s   _Min-NM:s   	s   
(   t   get_LCA_functionsR    R   R   R   R   R   R   t   splitt   lent   intt   appendt   sortt   dictt   zipt   gett   strt   joint   replacet   float(   t   samlinest   length_thresholdt   id_thresholdt   distanceR    R   R   R   R   R   R   t   nmst	   thresholdt   idst   lseqst   linet   textt   it   nmt   taxidt   seqt   l_seqt   lcat   familyt   idpt   stats(    (    sh   /mounts/lovelace/aDNA/DNA-Sequence-Analysis/aDNA/software-to-sort/getLCA-master/get_LCA_from_samlines.pyt   get_LCA_from_sam   sH    4"

%
<N(   R0   (    (    (    sh   /mounts/lovelace/aDNA/DNA-Sequence-Analysis/aDNA/software-to-sort/getLCA-master/get_LCA_from_samlines.pyt   <module>   s    