ó
£žbc           @   sr   d  d l  Z  d  d l Z d  d l m Z m Z m Z m Z m Z m Z d  d l	 m
 Z
 e
 e j ƒ Z d „  Z d S(   iÿÿÿÿN(   t   fastaparsert   N50t   plottert	   reportingt   qconfigt   qutils(   t
   get_loggerc         C   sÊ  t  j j | ƒ s" t  j | ƒ n  i g  d 6} x! | D] } g  | t j | ƒ <q6 Wt j ƒ  t j d ƒ t	 j
 |  ƒ } t | j ƒ  ƒ } g  }	 x0 | D]( } |	 j t t	 j
 | ƒ j ƒ  ƒ ƒ q˜ Wx×t t | | |	 ƒ ƒ D]½\ }
 \ } } } t | d t ƒ} t j | | ƒ \ } } t j | | ƒ } t j | | t j ƒ \ } } t j s t j | | ƒ \ } } t j | | t j ƒ \ } } t j | | ƒ } n  t j d t j |
 ƒ t j | ƒ d t t | ƒ ƒ d t | ƒ t j r| rd t | ƒ n d d	 t | ƒ t j r7| r7d
 t | ƒ n d ƒ t j | ƒ } | j t j  j! t | ƒ ƒ | j t j  j" t | ƒ ƒ | j t j  j# | ƒ | j t j  j$ | ƒ | j t j  j% | d  k	 r×d | n d  ƒ | j t j  j' | ƒ | j t j  j( | ƒ t j sÝ | j t j  j) | ƒ | j t j  j* | ƒ | j t j  j+ | d  k	 rdd | n d  ƒ | j t j  j, | ƒ | j t j  j- | ƒ qÝ qÝ Wt g  t. t/ | ƒ ƒ D] }
 t/ | |
 ƒ ^ q´ƒ } t j0 rd d l1 m2 } | j3 | | |	 ƒ n  t j4 r6t5 j6 |  | | t  j j7 | d ƒ d ƒ n  t5 j8 | | t j9 k | | | d d |	 ƒ t j s¹t5 j8 | | t j9 k | | | d d g  t. t/ | ƒ ƒ D] }
 | ^ q£ƒ n  t j d ƒ | S(   Nt   headers   Running NA-NGA calculation...t   reverses     s   , Largest alignment = s	   , NA50 = s
   , NGA50 = t    s	   , LA50 = s
   , LGA50 = s   %.1fiÿÿÿÿ(   t
   html_savert   cumulative_plots#   Cumulative length (aligned contigs)s	   /NAx_plott   NAxs
   /NGAx_plott   NGAxs   Done.(:   t   ost   patht   isdirt   mkdirR   t   name_from_fpatht   loggert   print_timestampt	   main_infoR    t   get_chr_lengths_from_fastafilet   sumt   valuest   appendt	   enumeratet   zipt   sortedt   TrueR   t   NG50_and_LG50t	   au_metricR   t   x_for_additional_Nxt   is_combined_reft   infot   index_to_strt   label_from_fpatht   strt   maxR   t   gett	   add_fieldt   Fieldst	   LARGALIGNt   TOTAL_ALIGNED_LENt   NA50R   t   auNAt   Nonet   LA50t   LAxt   NGA50R   t   auNGAt   LGA50t   LGAxt   ranget   lent   html_reportt   quast_libs.html_saverR
   t   save_assembly_lengthst
   draw_plotsR   R   t   joint   Nx_plott
   max_points(   t	   ref_fpatht   aligned_contigs_fpathst   output_dirpatht   aligned_lengths_listst   aligned_stats_dirpatht   report_dictt   contigs_fpatht   ref_chr_lengthst   reference_lengtht   assembly_lengthst   it   lenst   assembly_lent   sorted_lengthst   na50t   la50R-   t   naxt   laxt   nga50t   lga50t   ngaxt   lgaxR2   t   reportt   num_contigsR
   (    (    sF   /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_libs/aligned_stats.pyt   do   sl    
&(	q(,	,5		
%	3(   R   t	   itertoolst
   quast_libsR    R   R   R   R   R   t   quast_libs.logR   t   LOGGER_DEFAULT_NAMER   RV   (    (    (    sF   /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_libs/aligned_stats.pyt   <module>   s
   .