ó
QŽfXc           @   sÂ   d  d l  Z  d  d l  m Z d  d l Z d  d l Z d  d l Z d  d l Z d  d l Z d „  Z d „  Z d „  Z	 d „  Z
 d „  Z d d d	 „  ƒ  YZ d
 d d „  ƒ  YZ d d d „  ƒ  YZ d S(   iÿÿÿÿN(   t	   SeqRecordc         C   s¶  t  ƒ  } x9 t t | ƒ ƒ D]% } d g t | | ƒ d | | <q Wg  } xd|  D]\} | j | ƒ t | ƒ d k rR | d j r¥| d j | d | d j | d j | k  r| | d j | d j | d c d 7<| | d j | d j | d j | c d 8<q¥| d j | d | d j | d j | k  r¥| | d j | d j | d c d 7<| | d j | d j | d j | c d 8<q¥n  g  } qR qR W| S(   Ni    i   i   (   t   dictt   ranget   lent   appendt   proper_alignmentt   post   alent   tid(   t   samt   contigst   kt   covt   contigt   readst   rec(    (    sq   /home/psgendb/BIRCHDEV/pkg/SPAdes-3.13.0/linux-x86_64/share/spades/spades_pipeline/truspades/break_by_coverage.pyt   ConstructCoverage   s     	#1*41*7c         C   sÕ   t  ƒ  } x9 t t | ƒ ƒ D]% } d g t | | ƒ d | | <q Wx‰ |  D] } | j rL | j | d | j | j | k  rÍ | | j | j | d c d 7<| | j | j | j | c d 8<qÍ qL qL W| S(   Ni    i   (   R   R   R   R   R   R   R   (   R	   R
   R   R   R   R   (    (    sq   /home/psgendb/BIRCHDEV/pkg/SPAdes-3.13.0/linux-x86_64/share/spades/spades_pipeline/truspades/break_by_coverage.pyt   ConstructCoverageSingle'   s    	#	%"/c         C   sÖ   t  j j | ƒ r" t j | ƒ n  t  j | ƒ x  t t | ƒ ƒ D]Œ } t | d | | j	 d ƒ } d } xU t t |  | ƒ ƒ D]= } | |  | | 7} | j
 t | ƒ d t | ƒ d ƒ qƒ W| j ƒ  qB Wd  S(   Nt   /t   wi    t    s   
(   t   ost   patht   existst   shutilt   rmtreet   makedirsR   R   t   opent   idt   writet   strt   close(   R   R
   t   folderR   t   ft   curt   i(    (    sq   /home/psgendb/BIRCHDEV/pkg/SPAdes-3.13.0/linux-x86_64/share/spades/spades_pipeline/truspades/break_by_coverage.pyt
   OutputHist2   s    )c         C   s¡   t  ƒ  } x9 t t | ƒ ƒ D]% } d g t | | ƒ d | | <q WxU |  D]M } | j sL | | j | j c d 7<| | j | j | j c d 8<qL qL W| S(   Ni    i   (   R   R   R   t   is_unmappedR   R   R   (   R	   R
   R   t
   simple_covR   R   (    (    sq   /home/psgendb/BIRCHDEV/pkg/SPAdes-3.13.0/linux-x86_64/share/spades/spades_pipeline/truspades/break_by_coverage.pyt   ConstructSimpleCoverage>   s    	#	(c   	      C   sö   t  |  ƒ d } | d | k  r$ g  Sg  } d } d } d } x t | ƒ D] } | |  | 7} | d k rv | d 7} qI | | k r˜ t d | | ƒ } n, | | k rÄ | j | | | g ƒ | } n  d } qI W| j | t | | | | ƒ g ƒ | S(   Ni   i   i    (   R   R   t   maxR   t   min(	   R   R   t   min0t   lt   resultR"   t   cur_len0t
   prev_breakR#   (    (    sq   /home/psgendb/BIRCHDEV/pkg/SPAdes-3.13.0/linux-x86_64/share/spades/spades_pipeline/truspades/break_by_coverage.pyt   BreakContigH   s&    	
$t   ContigBreakerc           B   s#   e  Z d  „  Z d „  Z d „  Z RS(   c         C   sw   g  |  _  | |  _ | |  _ t |  j | | ƒ } x@ t t | ƒ ƒ D], } t | | | | ƒ } |  j  j | ƒ qC Wd  S(   N(   t
   part_list_R
   R	   R   R   R   R/   R   (   t   selfR
   R	   R   R*   R   R   t   parts(    (    sq   /home/psgendb/BIRCHDEV/pkg/SPAdes-3.13.0/linux-x86_64/share/spades/spades_pipeline/truspades/break_by_coverage.pyt   __init___   s    			c         C   sR   g  } xE |  j  |  j j | j ƒ D]' } | j | j | d | d ƒ ƒ q# W| S(   Ni    i   (   R1   R	   t   gettidR   R   t   subseq(   R2   R   R,   t   part(    (    sq   /home/psgendb/BIRCHDEV/pkg/SPAdes-3.13.0/linux-x86_64/share/spades/spades_pipeline/truspades/break_by_coverage.pyt   Breakj   s    #%c         C   s^   t  | d ƒ } x> |  j D]3 } x* |  j | ƒ D] } t j | | d ƒ q/ Wq W| j ƒ  d  S(   NR   t   fasta(   R   R
   R8   t   SeqIOR   R   (   R2   t   output_filet   outputR   t	   subcontig(    (    sq   /home/psgendb/BIRCHDEV/pkg/SPAdes-3.13.0/linux-x86_64/share/spades/spades_pipeline/truspades/break_by_coverage.pyt   OutputBrokenr   s
    (   t   __name__t
   __module__R4   R8   R>   (    (    (    sq   /home/psgendb/BIRCHDEV/pkg/SPAdes-3.13.0/linux-x86_64/share/spades/spades_pipeline/truspades/break_by_coverage.pyR0   ^   s   		t   PatternBreakerc           B   s,   e  Z d  „  Z d „  Z d „  Z d „  Z RS(   c         C   s   | |  _  | |  _ | |  _ d  S(   N(   t   patternt
   rc_patternt   max_cut(   R2   RB   RC   RD   (    (    sq   /home/psgendb/BIRCHDEV/pkg/SPAdes-3.13.0/linux-x86_64/share/spades/spades_pipeline/truspades/break_by_coverage.pyR4   z   s    		c         C   s‘   | j  |  j ƒ } | j  |  j ƒ } | d k r? t | ƒ } n  | d k rZ t | ƒ } n  t | | ƒ t |  j ƒ } | |  j k  r‰ | Sd Sd  S(   Niÿÿÿÿi    (   t   findRB   RC   R   R)   RD   (   R2   t   seqt   l1t   l2R+   (    (    sq   /home/psgendb/BIRCHDEV/pkg/SPAdes-3.13.0/linux-x86_64/share/spades/spades_pipeline/truspades/break_by_coverage.pyt   FindLeftPos   s    c         C   sˆ   | j  |  j ƒ } | j  |  j ƒ } | d k r9 d } n  | d k rN d } n  t | | ƒ } | t | ƒ |  j k rz | St | ƒ Sd  S(   Niÿÿÿÿi    (   t   rfindRB   RC   R(   R   RD   (   R2   RF   RG   RH   R+   (    (    sq   /home/psgendb/BIRCHDEV/pkg/SPAdes-3.13.0/linux-x86_64/share/spades/spades_pipeline/truspades/break_by_coverage.pyt   FindRightPosŒ   s    		c         C   sU   t  | ƒ d |  j k  r g  S|  j | j ƒ |  j | j ƒ } } | j | | ƒ g S(   Ni   (   R   RD   RI   RF   RK   R6   (   R2   R   R+   t   r(    (    sq   /home/psgendb/BIRCHDEV/pkg/SPAdes-3.13.0/linux-x86_64/share/spades/spades_pipeline/truspades/break_by_coverage.pyR8   ™   s    %(   R?   R@   R4   RI   RK   R8   (    (    (    sq   /home/psgendb/BIRCHDEV/pkg/SPAdes-3.13.0/linux-x86_64/share/spades/spades_pipeline/truspades/break_by_coverage.pyRA   y   s   			t   NBreakerc           B   s   e  Z d  „  Z d „  Z RS(   c         C   s   | |  _  d  S(   N(   t   min_N(   R2   RN   (    (    sq   /home/psgendb/BIRCHDEV/pkg/SPAdes-3.13.0/linux-x86_64/share/spades/spades_pipeline/truspades/break_by_coverage.pyR4       s    c         C   s  g  } d } d } x0 | t  | ƒ k  rD | | d k rD | d 7} q Wx— | t  | ƒ k  rÞ | } x0 | t  | ƒ k  r’ | | d k r’ | d 7} qc W| | |  j k rÈ | j | j | | ƒ ƒ | } n  t | | d ƒ } qH W| t  | ƒ k r| j | j | t  | ƒ ƒ ƒ n  | S(   Ni    t   Ni   (   R   RN   R   R6   R(   (   R2   R   R,   t
   last_breakR   t   rpos(    (    sq   /home/psgendb/BIRCHDEV/pkg/SPAdes-3.13.0/linux-x86_64/share/spades/spades_pipeline/truspades/break_by_coverage.pyR8   £   s     %%	"(   R?   R@   R4   R8   (    (    (    sq   /home/psgendb/BIRCHDEV/pkg/SPAdes-3.13.0/linux-x86_64/share/spades/spades_pipeline/truspades/break_by_coverage.pyRM   Ÿ   s   	(    (    (    (   R:   R    t   sysR   R   t
   sam_parsert	   itertoolsR   R   R$   R'   R/   R0   RA   RM   (    (    (    sq   /home/psgendb/BIRCHDEV/pkg/SPAdes-3.13.0/linux-x86_64/share/spades/spades_pipeline/truspades/break_by_coverage.pyt   <module>
   s   				
	&