ó
£žbc           @€  sŠ   d  d l  m Z d  d l Z d  d l m Z d  d l m Z m Z m Z d  d l	 m
 Z
 d  d l m Z m Z m Z d „  Z d „  Z d S(	   iÿÿÿÿ(   t   with_statementN(   t   join(   t	   reportingt   qconfigt   qutils(   t	   parse_gff(   t   run_parallelt   call_subprocesst   is_non_empty_filec         C€  so   t  t j d d d ƒ } t | ƒ r( d  St | d d | d t | ƒ |  g d t | d ƒ d t | d	 ƒ ƒd  S(
   Nt   barrnapt   bins   --quiets   -ks	   --threadst   stdoutt   wt   stderrt   a(   R   R   t   LIBS_LOCATIONR   R   t   strt   open(   t   contigs_fpatht	   gff_fpatht	   log_fpatht   threadst   kingdomt   barrnap_fpath(    (    sD   /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_libs/run_barrnap.pyt   run   s
    $c         C€  s‘  | j  ƒ  | j d ƒ t t |  ƒ t j ƒ } t d t j | ƒ } t j j	 | ƒ sg t j
 | ƒ n  t | d ƒ } | j d | d ƒ t j rš d n d } g  |  D]" } t | t j | ƒ d ƒ ^ q§ } g  t |  | ƒ D]! \ } }	 | |	 | | | f ^ qß }
 t t |
 t j ƒ t d	 „  | Dƒ ƒ s@| j d
 ƒ d  Sx=t t |  | ƒ ƒ D]&\ } \ } }	 t t |	 ƒ d ƒ } t j | ƒ } t j j |	 ƒ sÁ| j d | d | d ƒ qVn  t g  | D]. } d | j k rËd | j d k rË| ^ qËƒ } t | ƒ } | j t j j d | | | f ƒ | j d t j | ƒ d t | ƒ ƒ | j d t j | ƒ d |	 ƒ qVW| j d ƒ d  S(   Ns   Running Barrnap...i   s   barrnap.logs   Logging to s   ...t   bact   euks   .rna.gffc         s€  s   |  ] } | Vq d  S(   N(    (   t   .0t   fpath(    (    sD   /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_libs/run_barrnap.pys	   <genexpr>)   s    s6   Failed predicting the location of ribosomal RNA genes.t   rrnas   Failed running Barrnap for s   . See s    for information.t   productt   partials   %s + %s parts     s     Ribosomal RNA genes = s     Predicted genes (GFF): s   Done.(    t   print_timestampt   infot   mint   lenR   t   max_threadst   maxt   ost   patht   isdirt   makedirsR   t
   prokaryoteR   t   label_from_fpath_for_fnamet   zipR   R   t   anyt	   enumerateR   R   R   t   gett   isfilet   errort
   attributest	   add_fieldt   Fieldst	   RNA_GENESt   index_to_strR   (   t   contigs_fpathst
   output_dirt   loggert   n_jobsR   R   R   R   t
   gff_fpathsR   t   barrnap_argst   indext   genest   reportt   genet
   part_countt   total_count(    (    sD   /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_libs/run_barrnap.pyt   do   s6    
/7(A$(&(   t
   __future__R    R&   t   os.pathR   t
   quast_libsR   R   R   t   quast_libs.genes_parserR   t   quast_libs.qutilsR   R   R   R   RC   (    (    (    sD   /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_libs/run_barrnap.pyt   <module>   s   	