ó
£žbc           @€  s2  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  d l m Z m	 Z	 m
 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 d  d l m Z d  d	 l m Z m Z m Z e e	 j ƒ Z e Z d
 „  Z d „  Z  d „  Z! d „  Z" e d „ Z# d „  Z$ d S(   iÿÿÿÿ(   t   with_statementN(   t	   reportingt   qconfigt   qutils(   t   open_gzipsafe(   t
   read_fastat   write_fastat   rev_comp(   t   add_genes_to_fasta(   t   Gene(   t
   get_logger(   t   compile_toolt   get_path_to_programt   run_parallelc      
   C€  sl   t  | d ƒ } | j d ƒ x? |  D]7 } t | ƒ # } | j t j | d d ƒ ƒ Wd QXq# W| j ƒ  | S(   s<   Merges all GFF files into a single one, dropping GFF header.t   ws   ##gff-version 3
i   N(   R   t   writet   opent
   writelinest	   itertoolst   islicet   Nonet   close(   t   gffst   out_patht   out_filet   gff_patht   gff_file(    (    s@   /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_libs/glimmer.pyt
   merge_gffs   s    &
c      
   c€  sÇ   t  |  ƒ } t j t t d „  | ƒ ƒ d d ƒ} xƒ | D]{ \	 } } } } } } }	 }
 } | d k rm q: n  t d „  | j d ƒ Dƒ ƒ } | | j d ƒ t | ƒ t | ƒ |	 f Vq: W| j	 ƒ  d  S(   Nc         S€  s   |  j  d ƒ S(   Nt   #(   t
   startswith(   t   l(    (    s@   /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_libs/glimmer.pyt   <lambda>*   s    t	   delimiters   	t   mRNAc         s€  s   |  ] } | j  d  ƒ Vq d S(   t   =N(   t   split(   t   .0t   kv(    (    s@   /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_libs/glimmer.pys	   <genexpr>0   s    t   ;t   Name(
   R   t   csvt   readert   listt   filtert   dictR#   t   gett   intR   (   R   R   t   rt   indext   _sourcet   typet   startt   endt   scoret   strandt   phaset   extrat   attrs(    (    s@   /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_libs/glimmer.pyt	   parse_gff(   s    	(-c   !      €  s  ‡  ‡ ‡ ‡ f d †  } t  j j |  d d ƒ ‰ i  }	 g  }
 t j d | ƒ } x¶ t t | ƒ ƒ D]¢ \ } \ } } t | ƒ } | t j	  } t  j j | | d ƒ } t  j j | | d ƒ } t
 | | | f g ƒ | | | ƒ d k ra |
 j | ƒ | |	 | <qa qa W|
 sd S| d } t |
 | ƒ } t ƒ  d } } g  } xç t | ƒ D]Ù \ } } } } } | d	 7} | d
 k r|	 | | d	 | !} n t |	 | | d	 | !ƒ } | | k rÇ| j | ƒ n  t d | d | d | d | d | ƒ } | j d	 k o| j t |	 | ƒ k  | _ | j | ƒ qMWg  | D]> } t g  | D]% } | j rA| j | j | k ^ qAƒ ^ q1} g  | D]> } t g  | D]% } | j sŒ| j | j | k ^ qŒƒ ^ q|} t rà| d }  t | |  ƒ n  t j sùt j | ƒ n  | | t | ƒ | | | f S(   Nc         €  sg   t  ˆ  d ƒ R } t j ˆ |  d ˆ d d | g d | d | d d t j ˆ ƒ d ƒ} | SWd  QXd  S(	   Nt   as   -ds   -gs   -ot   stdoutt   stderrt   indents     (   R   R   t   call_subprocesst   index_to_str(   t   contig_patht   tmp_patht   err_filet   return_code(   t   err_pathR0   t   tool_exec_fpatht   trained_dir(    s@   /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_libs/glimmer.pyt   run6   s    t   trainedt   arabidopsist   dirs   .fastas   .gffi    s
   _genes.gffi   t   +t   contigR3   R4   R6   t   seqs   _genes.fasta(   NNNNNN(   t   ost   patht   joint   tempfilet   mkdtempt	   enumerateR   t   strR   t   MAX_CONTIG_NAME_GLIMMERR   t   appendR   R   t   setR:   R   t   addR	   R3   R4   t   lent   is_fullt   sumt   OUTPUT_FASTAR   R   t   debugt   shutilt   rmtree(!   t   tool_dirRF   t   fasta_fpatht	   out_fpatht   gene_lengthsRE   t   tmp_dirR0   RH   t   contigsR   t   base_dirt   seq_numt   indRN   RA   R   t   out_gff_fpatht   out_gff_patht   uniquet   totalt   genesRM   t   gene_idR3   R4   R6   t   gene_seqt   genet	   thresholdt   full_cntt   partial_cntt   out_fasta_fpath(    (   RE   R0   RF   RG   s@   /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_libs/glimmer.pyt
   glimmerHMM5   sL    
%
"
'+KK
	c      	   C€  s  t  j | ƒ } t  j | ƒ } t j d t  j |  ƒ | ƒ t j j | | d ƒ }	 t j j | | d ƒ }
 t	 | | | |	 | |
 | |  ƒ \ } } } } } } | rt j d t  j |  ƒ d t
 | ƒ d t
 | ƒ d ƒ t j d t  j |  ƒ d | ƒ n  | | | | f S(   Ns     t   _glimmers   _glimmer.stderrs
     Genes = s	    unique, s    totals     Predicted genes (GFF): (   R   t   label_from_fpatht   label_from_fpath_for_fnamet   loggert   infoR@   RO   RP   RQ   Rv   RU   (   R0   t   contigs_fpathRd   t   out_dirpatht   tool_dirpathRF   t   tmp_dirpatht   assembly_labelt   corr_assembly_labelRc   t	   err_fpathRk   Rn   Rl   Rm   t
   full_genest   partial_genes(    (    s@   /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_libs/glimmer.pyt   predict_geneso   s    	*:%c         C€  sk   t  j j t j d ƒ } t  j j | d ƒ } t d | ƒ s^ t d | d g d |  d | ƒn  t d | ƒ S(   Nt   glimmert   srct
   glimmerhmmt
   GlimmerHMMs   ../glimmerhmmRz   t
   only_clean(   RO   RP   RQ   R   t   LIBS_LOCATIONR   R   (   Rz   RŠ   R~   t   tool_src_dirpath(    (    s@   /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_libs/glimmer.pyt   compile_glimmer…   s
    "c      	   C€  sa  t  j ƒ  t  j d ƒ t j j t j d ƒ } t j j | d ƒ } t t  ƒ } | sZ d  St j j	 | ƒ s| t j
 | ƒ n  t j j	 | ƒ sž t j
 | ƒ n  t t |  ƒ t j ƒ } g  t |  ƒ D]' \ } } | | | | | | | f ^ qÃ }	 t t |	 | ƒ \ }
 } } } t ƒ  } xt |  ƒ D]\ } } t j | ƒ } t j | ƒ } |
 | | | <| | d  k	 r‰| j t j j | | ƒ n  | | d  k	 rìg  t | | | | ƒ D] \ } } d | | f ^ q±} | j t j j | ƒ n  | | d  k r$| | d  k r$t  j d | t j s(d n d ƒ q$q$Wt j sPt j | ƒ n  t  j d ƒ | S(	   Ns   Running GlimmerHMM...R†   t   tmps   %s + %s parts   Failed running Glimmer for %s. s4   Run with the --debug option to see the command line.t    s   Done.(    Rz   t   print_timestampt	   main_infoRO   RP   RQ   R   R‹   R   t   isdirt   makedirst   minRZ   t   max_threadsRT   R   R…   R,   R   R-   R   Rx   R   t	   add_fieldt   Fieldst   PREDICTED_GENES_UNIQUEt   zipt   PREDICTED_GENESt   errorR^   R_   R`   (   t   contigs_fpathsRd   R}   R~   R   RF   t   n_jobsR0   R|   t   parallel_argst
   genes_listRl   Rƒ   R„   t   genes_by_labelst   it   reportt   labelRs   Rt   Rn   (    (    s@   /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_libs/glimmer.pyt   doŽ   sB    
7	: 	(%   t
   __future__R    RO   RR   R   R(   R_   t
   quast_libsR   R   R   t   quast_libs.ca_utils.miscR   t   quast_libs.fastaparserR   R   R   t   quast_libs.genemarkR   t   quast_libs.genes_parserR	   t   quast_libs.logR
   t   quast_libs.qutilsR   R   R   t   LOGGER_DEFAULT_NAMERz   t   FalseR]   R   R:   Rv   R…   R   R¤   (    (    (    s@   /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_libs/glimmer.pyt   <module>   s(   			:		