ó
£žbc           @€  sƒ   d  d l  m Z d  d l m Z d  d l m Z m Z m Z d  d l m	 Z	 m
 Z
 d „  Z d „  Z d „  Z d „  Z d	 „  Z d
 S(   iÿÿÿÿ(   t   with_statement(   t   defaultdict(   t   fastaparsert   qconfigt   qutils(   t	   Alignmentt   Contigc   (   #   C€  s}  g  } g  } t  |  ƒ S} t t ƒ } t t ƒ } d  } d  }	 d  }
 d  } d  } d  } d  } d  } d  } d  } xõt | ƒ D]ç\ } } | j d d ƒ j d ƒ } | d k r9| j d ƒ }	 | j d ƒ }
 | j d ƒ } | j d ƒ } | j d	 ƒ } | j d
 ƒ } | j d ƒ } | j d ƒ } | j d ƒ } q| | r’| d d k r’| \ } } } } t d | d t	 | ƒ d | ƒ } | j
 | ƒ q| | rÄt | ƒ d k  rÄ| | j
 | j ƒ  ƒ q| | r| t | ƒ d k r| | |	 | |
 | | | | | | | | | | | | | | f	 \	 } } } } } } } }  }! t	 | ƒ t	 | ƒ t	 | ƒ t	 | ƒ f \ } } } } | | j | ƒ pˆd }" | |" d }# | |" d }$ |# |$ | | d k  }% | }& t d | d |# d |$ d | d | d |% d | d | d |& d | d | d |! d k ƒ }' |  |' _ |' j rB| | j
 |' ƒ n | | j
 |' ƒ | j
 |' ƒ q| q| WWd  QX| | | | f S(    Ns   
t    s   	i    t   S1t   E1t   S2t   E2t	   ReferenceR   t   IDYt	   Ambiguoust
   Best_groupt   CONTIGt   namet   sizet   contig_typei   i   t   startt   endt   unshifted_startt   unshifted_endt   is_rct   start_in_contigt   end_in_contigt   position_in_reft   ref_namet   idyt   is_best_sett   True(   t   openR   t   listt   Nonet	   enumeratet   replacet   splitt   indexR   t   intt   appendt   lent   stripR   t	   ambiguousR   ((   t   report_fpatht	   ref_namest   cumulative_ref_lengthst   aligned_blockst   contigst   report_filet   misassembled_id_to_structuret   ambiguity_alignmentst	   contig_idt	   start_colt   end_colt   start_in_contig_colt   end_in_contig_colt   ref_colt
   contig_colt   idy_colt	   ambig_colt   best_colt   it   linet
   split_linet   _R   R   R   t   contigR   R   R   R   R   R   t	   ambiguityt   is_bestt	   cur_shiftR   R   R   R   t   block(    (    sF   /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_libs/icarus_parser.pyt   parse_aligner_contig_report   sj    !D$		c         C€  sR   g  } xE t  j |  ƒ D]4 \ } } t d | d t | ƒ ƒ } | j | ƒ q W| S(   NR   R   (   R   t
   read_fastaR   R)   R(   (   t   contigs_fpathR0   R   t   seqRB   (    (    sF   /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_libs/icarus_parser.pyt   parse_contigs_fpathQ   s
    c      	   C€  s  |  s
 d St t ƒ } t t ƒ } g  } t |  d ƒ Ó} t ƒ  } xŒ | D]„ }	 | r‚ g  | D] }
 | |
 |	 k r] |
 ^ q] } n$ t | ƒ d k r | } n	 |	 g } x | D] }
 |	 | |
 <q­ W| j | ƒ qJ Wg  t t | ƒ ƒ D] } g  ^ qå } d  } x t	 | ƒ D] \ } } | j
 ƒ  } | j d ƒ rc| d d } | | k rZ| j | ƒ n d  } q
| d  k	 r
t t | d ƒ ƒ } | | j | ƒ q
q
Wx9 t	 | ƒ D]+ \ } }
 | |
 } | | j | | ƒ qªWx* | j ƒ  D] \ } } t | ƒ | | <qæWWd  QX| | f S(   Nt   ri   t   #i    (   NN(   R"   R   R!   R'   R    t   dictR)   t   extendt   rangeR#   R%   t
   startswithR&   t   floatR(   t   itemst   max(   t	   cov_fpatht	   chr_namest   chr_full_namest   contig_names_by_refst   cov_datat	   max_deptht   chr_contigst   coveraget   contig_to_chrt   chrRB   R0   t   xt   data_by_contigt   chrom_indexR&   R?   t   fst   chr_namet   depthR>   t   chromt   depths(    (    sF   /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_libs/icarus_parser.pyt   parse_cov_fpathY   s@    	,		%$
c         C€  s¹  d } |  rµ| d 7} g  } x…|  D]}} t  | j ƒ d k rD q# n  | d 7} x5| j D]*} | j r‚ | j | j k r‚ | j n | j } | | j k r§ | j | n d  } | sX | | k rÆ qX n  | j | ƒ } | | }	 | j |	 }
 | j |	 } | d t	 | j
 ƒ d t	 | j ƒ d t	 | j ƒ d t	 |
 ƒ d	 t	 | ƒ d
 t	 | j ƒ d t	 | j ƒ d t	 | ƒ d 7} qX W| j | j ƒ | d 7} q# W| d  d } n  | S(   Ns   var features_data = [];
s   features_data = [ i    s   [ s   {name: "s
   ", start: s   , end: s   ,corr_start: s   ,corr_end: s   , id_: "s	   ",kind: "s   ", chr:s   },s   ],iÿÿÿÿs   ];
(   R)   t   region_listt
   chromosomet   chr_names_dictt   seqnameR"   R&   R   R   t   strR   t   idt   kindR(   (   t   featuresR.   R-   t   features_datat   containers_kindt   feature_containert   regionRe   t   ref_idRE   t
   corr_startt   corr_end(    (    sF   /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_libs/icarus_parser.pyt   parse_features_data}   s0    

$	"
Šc         C€  s¥   | s
 d  Sx” | j  ƒ  D]† \ } } | s/ q n  t j rU t d „  |  | Dƒ ƒ } n t d „  |  | Dƒ ƒ } x+ | D]# } | | j } | j j | ƒ qv Wq Wd  S(   Nc         s€  s%   |  ] } | j  t j  | f Vq d  S(   N(   R   R   t   MAX_CONTIG_NAME_GLIMMER(   t   .0RB   (    (    sF   /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_libs/icarus_parser.pys	   <genexpr>    s    c         s€  s   |  ] } | j  | f Vq d  S(   N(   R   (   Ry   RB   (    (    sF   /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_libs/icarus_parser.pys	   <genexpr>¢   s    (   RS   R   t   glimmerRN   RB   t   genesR(   (   t   contigs_by_assembliest   genes_by_labelst   labelR{   R0   t   geneRB   (    (    sF   /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_libs/icarus_parser.pyt   parse_genes_data™   s    	N(   t
   __future__R    t   collectionsR   t
   quast_libsR   R   R   t   quast_libs.icarus_utilsR   R   RG   RK   Rg   Rw   R€   (    (    (    sF   /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_libs/icarus_parser.pyt   <module>
   s   	?		$	