ó
QŽfXc           @   sj   d  d l  Z  d  d l Z d  d l Z d  d l Z e  j d ƒ Z d d „ Z d „  Z d „  Z d „  Z	 d S(   iÿÿÿÿNs   ([0-9]*)([MIDNSHP])i    c         c   s  |  d k r6 x# t  | ƒ D] } | | | f Vq Wd  S|  d k rF d  Sd } | } x¯ t j |  ƒ D]ž \ } } | rƒ t | ƒ } n d } | d k rÎ xh t  | ƒ D]% } | | f V| d 7} | d 7} q¢ Wqb | d k rç | | 7} qb | d k rb | | 7} qb qb Wd  S(   Nt   =t   Xi    i   t   Mt   DPNt   IS(   t   ranget   patternt   findallt   int(   t   cigart   lent   post   it   curt   currt   nt   c(    (    sp   /home/psgendb/BIRCHDEV/pkg/SPAdes-3.13.0/linux-x86_64/share/spades/spades_pipeline/truspades/generate_quality.pyt   parse   s*    
c         C   sö   g  |  D]1 } g  t  t | ƒ ƒ D] } d d g ^ q  ^ q } x± | D]© } | j rE x— t | j | j | j d ƒ D]s \ } } | j | |  | j j | k rt | | j | d c d 7<| | j | d c t	 | j
 | ƒ 7<qt qt WqE qE W| S(   Ni    i   (   R   R
   t   proper_alignmentR   R	   t   alenR   t   seqt   tidt   ordt   qual(   t   contigst   samt   contigR   R   t   rect   seq_post
   contig_pos(    (    sp   /home/psgendb/BIRCHDEV/pkg/SPAdes-3.13.0/linux-x86_64/share/spades/spades_pipeline/truspades/generate_quality.pyt   CollectQuality&   s    >	,!6c         C   sÂ   x» t  t |  ƒ ƒ D]§ } d } t d ƒ g t |  | ƒ } xe t  t |  | ƒ ƒ D]M } | | | } | d d k r– t | d | d ƒ | | <qS | d 7} qS Wd j | ƒ |  | _ q Wd  S(   Ni    i!   i   t    (   R   R
   t   chrt   joinR   (   R   R   R   t   cntt	   qual_listR   t   q(    (    sp   /home/psgendb/BIRCHDEV/pkg/SPAdes-3.13.0/linux-x86_64/share/spades/spades_pipeline/truspades/generate_quality.pyt   CountContigQuality0   s    c         C   s    t  |  | ƒ } t |  | ƒ d  S(   N(   R   R%   (   R   R   R   (    (    sp   /home/psgendb/BIRCHDEV/pkg/SPAdes-3.13.0/linux-x86_64/share/spades/spades_pipeline/truspades/generate_quality.pyt   GenerateQuality=   s    (
   t   ret   syst	   itertoolst
   sam_parsert   compileR   R   R   R%   R&   (    (    (    sp   /home/psgendb/BIRCHDEV/pkg/SPAdes-3.13.0/linux-x86_64/share/spades/spades_pipeline/truspades/generate_quality.pyt   <module>   s   	
	