
    DUf
                        d dl Z d dlZddlmZ  ej                    d             Ze                                 ej        d          d                         Ze                                 ej        d           ej        de		           ej
        d
dd          d                                                 Ze                                 ej        d           ej        d           ej        d          d                                                 Ze                                 ej        d           ej        d           ej
        ddd          d                                                 Ze                                 ej        d           ej        d          d                                     ZdS )    N   )clic                      dS )z2
    Utilities for binned genome assemblies.

    N r       Q/var/www/html/software/conda/lib/python3.11/site-packages/cooltools/cli/genome.pygenomer	      s      r   dbc                 ~    dd l }|                    |           }t          |                    d                     d S )Nr   	)sep)bioframefetch_chromsizesprintto_csv)r
   r   
chromsizess      r   r   r      sE     OOO**2..J	*



%
%&&&&&r   chromsizes_pathbinsize)typez--all-namesz`Parse all chromosome names from file, not only default r"^chr[0-9]+$", r"^chr[XY]$", r"^chrM$". T)helpis_flagc                     dd l }|                    | |           }|                    ||          }t          |                    dd                     d S )Nr   filter_chromsr   Fr   index)r   read_chromsizesbinnifyr   r   )r   r   	all_namesr   r   binss         r   r   r      si     OOO))I *  J J00D	$++$e+
,
,-----r   
fasta_pathenzyme_namec                 ~   dd l }|                    | d          }|                    |dd          }|j                            |                                          s#t          d                    | |                    |                    ||          }t          |
                    dd	                     d S )
Nr   Fr   pyfaidxTengineas_raw4Some chromosomes mentioned in {} are not found in {}r   r   )r   r   
load_fastar   isinall
ValueErrorformatdigestr   r   )r   r!   r"   r   r   fasta_recordsfragss          r   r.   r.   )   s    
 OOO))/)OOJ''
9T'RRM  //3355 
##)6/:#F#F
 
 	
 OOM;77E	%,,4u,
-
-.....r   	bins_pathz--mapped-only)r   defaultc                    dd l }dd l}| dk    rt          j        } |                    |           }|d                                         }|                    |dd          t          fd|D                       r#t          d	                    | |                    |
                    ||          }t          |                    d	d
                     d S )Nr   -chromr$   Tr%   c              3   D   K   | ]}|                                 vV  d S )N)keys).0r5   r/   s     r   	<genexpr>zgc.<locals>.<genexpr>H   s4      
F
F5**,,,
F
F
F
F
F
Fr   r(   r   Fr   )r   pandassysstdin
read_tableuniquer)   anyr,   r-   frac_gcr   r   )r1   r!   mapped_onlyr   pdr    chromosomesr/   s          @r   gcrD   ;   s    
 OOOCI	==##Dw-&&((K''
9T'RRM

F
F
F
F+
F
F
FFF 
##)6)Z#@#@
 
 	
 D-==D	$++$e+
,
,-----r   c                     ddl }ddl}|                    |           }|                    ||          }t	          |                    dd                     dS )z
    BINS_PATH is the path to bintable.

    DB is the name of the genome assembly.
    The gene locations will be automatically downloaded from teh UCSC goldenPath.
    r   Nr   Fr   )r   r:   r=   frac_gene_coverager   r   )r1   r
   r   rB   r    s        r   genecovrG   Q   sc     OOO==##D&&tR00D	$++$e+
,
,-----r   )r;   click r   groupr	   commandargumentr   intoptionr   r.   rD   rG   r   r   r   <module>rO      sH   



           ' '  ' !""	$$$	k  
. .  %$ #" . !""/ /   #" / otT:::. . ;:   .$ . .   . . .r   