ó
£žbc           @   s|   d  d l  Z  d  d l m Z m Z m Z m Z d  d l m Z d  d l m	 Z	 e	 e j
 ƒ Z d „  Z d „  Z d „  Z d S(   iÿÿÿÿN(   t   plottert	   reportingt   qconfigt   qutils(   t
   print_file(   t
   get_loggerc         C   s¦  g  } |  } i d d 6| d 6} | j  | ƒ g  }	 x9 t | ƒ D]+ }
 i | |
 d 6g  d 6} | j  | ƒ q@ Wx't |  ƒ D]\ }
 } |	 j  g  ƒ d  g t | ƒ } t j j | | | ƒ } | t j	 k rö t j j t j j
 | ƒ | | ƒ } n  t j j | ƒ rLt | d ƒ } g  | j ƒ  j d ƒ D] } | j ƒ  ^ q-} | | k r'g  | j ƒ  j d ƒ D] } | j ƒ  ^ qg} d  g t | ƒ } x´ t | ƒ D] } | } | d rŸ| | j | ƒ j ƒ  d } g  | j ƒ  j d ƒ D] } | j ƒ  ^ qè} | j | d ƒ } | | | <qŸqŸWqL| t j	 k rL| j |
 ƒ q| qLn  xF t | ƒ D]8 } | | d d j  | | ƒ |	 d j  | | ƒ qYWq| W|	 | | f S(	   Nt
   Referencest
   metricNamet   valuest   rs   	i    i   iÿÿÿÿ(   t   appendt   ranget	   enumeratet   Nonet   lent   ost   patht   joinR   t   not_aligned_namet   dirnamet   existst   opent   readlinet   splitt   stript   indext   pop(   t   full_ref_namest   metrict   contigs_numt   labelst   output_dirpatht   report_fnamet   all_rowst	   ref_namest   rowt   resultst   it   ref_namet   cur_resultst   results_fpatht   results_filet   st   columnst   next_valuest   jR   t   metr_rest   index_contig(    (    sL   /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_libs/create_meta_summary.pyt   get_results_for_metric   sD    '..
.	c         C   sZ   t  j j |  | ƒ } t | d ƒ } g  | j ƒ  j d ƒ D] } | j ƒ  ^ q: } | d S(   NR	   s   	i   (   R   R   R   R   R   R   R   (   t   combined_output_dirpathR    R(   R)   R*   R   (    (    sL   /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_libs/create_meta_summary.pyt
   get_labels5   s    .c   !      C   sy  t  | t j d ƒ } t | ƒ } t j j ƒ  }	 xZ d |	 d d g D]F }
 t j j t j j	 | |
 ƒ ƒ sD t j
 t j j	 | |
 ƒ ƒ qD qD WxÂ| D]º} t | t ƒ s• | j d d ƒ j d d ƒ j d	 d
 ƒ j d d ƒ j d d ƒ } t j j	 | d | d ƒ } t j j	 | d | d ƒ } t j j	 | d | d ƒ } t j j	 | |	 | ƒ } t | | | | | t j d ƒ \ } } } | s• t d „  | Dƒ ƒ r¦q• n  | rOi d d 6g  t d t | ƒ ƒ D] } | | d ^ qÌd 6g } xˆ t t | d d ƒ ƒ D]l } g  } x6 t d t | ƒ ƒ D] } | j | | d | ƒ q*W| j i | d d | d 6| d 6ƒ qWt | | ƒ t j | | ƒ t j | | ƒ t } t j | ƒ t j j j k rÒt } n  d  } | t j j t j j t j j  t j j! g k rd } no | t j j" k r,d } nT | t j j# t j j$ t j j% t j j& g k red } n | t j j' k r€d } n  t( j) |  | | | | | d | d | d | d t d t* ƒ| t j j+ k rLg  } t j j	 t j, t j d d ƒ } | d  t j- k r| d   } n  xX | D]P } t | | t t j j. ƒ | | | | ƒ \ } } } | r| j | ƒ qqW| rIg  } xf t | ƒ D]X } t j j	 | |	 t/ j0 | | ƒ d ƒ } | j t( j1 | | | | d | | ƒƒ q‰Wt j2 rFd  d! l3 m4 }  | d  t j- k r| d   } n  | rC|  j5 |  | | | | ƒ qCqFqIqLqOq• q• Wt* j6 d ƒ t* j6 d" | d# ƒ d  S($   Ns   .tsvt   TXTt   TEXt   TSVs    (%)t    t   #t   nums   >=t   get    t   _t   's   .txts   .texc         s   s#   |  ] } | D] } | Vq q d  S(   N(    (   t   .0t   resultt   value(    (    sL   /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_libs/create_meta_summary.pys	   <genexpr>L   s    t
   AssembliesR   i   R   i    s   Total lengths   Aligned lengths   Contig lengths   Alignment lengtht   titlet   reverset   yaxis_titlet   print_all_refst   loggert   _misassembliesiÿÿÿÿ(   t
   html_saversf     Text versions of reports and plots for each metric (for all references and assemblies) are saved to t   /(7   R2   R   t   report_prefixR   t   plot_extensiont   upperR   R   t   isdirR   t   mkdirt
   isinstancet   tuplet   replaceR0   t   transposed_report_prefixt   allR   R
   R   R   t   save_tsvt   save_text   Falset   get_qualityt   Fieldst   Qualityt   MORE_IS_BETTERt   TrueR   t   TOTALLENt   TOTALLENS__FOR_1000_THRESHOLDt   TOTALLENS__FOR_10000_THRESHOLDt   TOTALLENS__FOR_50000_THRESHOLDt   TOTAL_ALIGNED_LENt
   LARGCONTIGt   N50t   NGA50t   MIS_EXTENSIVE_BASESt	   LARGALIGNR    t   draw_meta_summary_plotRE   t
   MISASSEMBLt    detailed_contigs_reports_dirnameR   t   TABR   t   slugifyt$   draw_meta_summary_misassemblies_plott   html_reportt   quast_libs.html_saverRG   t   save_meta_misassembliest	   main_info(!   t
   html_fpathR   R1   t   output_dirpath_per_reft   metricst   misassembly_metricsR"   R   R   t   plots_dirnamet   extR   t   metric_fnamet   summary_txt_fpatht   summary_tex_fpatht   summary_tsv_fpatht   summary_plot_fnameR$   R!   t   cur_ref_namesR%   t   transposed_tableR   R-   RB   t   y_labelt   mis_resultsR    t   misassembly_metrict   json_pointst
   contig_numt
   plot_fpathRG   (    (    sL   /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_libs/create_meta_summary.pyt   do<   sŽ    !#B+
7!					)		/(   R   t
   quast_libsR    R   R   R   t   quast_libs.ca_utils.miscR   t   quast_libs.logR   t   LOGGER_META_NAMERE   R0   R2   R‚   (    (    (    sL   /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_libs/create_meta_summary.pyt   <module>	   s   "	%	