ó
ÿfmSc           @   sˆ   d  d l  Z  d  d l m Z d  d l m Z e j d ƒ rM e j d ƒ Z n d Z d e Z d „  Z d „  Z	 d	 „  Z
 e d
 „ Z d S(   iÿÿÿÿN(   t   Genome(   t   environt   CISTEMATIC_ROOTs   /proj/genomes"   %s/S_purpuratus/spurpuratus.genedbc         C   sÙ  g  } d } t  d d |  ƒ} t | d ƒ } | j ƒ  } x| d k rÊg  } d } | j ƒ  } d | k ry | d }	 n | d j ƒ  }	 |	 j d	 ƒ }
 |
 d } | j ƒ  } xU | d k r| d d
 k r| j ƒ  } | t | ƒ 7} | j | ƒ | j ƒ  } q± Wt j | d ƒ } | d k  red | GH| j	 d | f | d t
 | ƒ ƒ | j | | d ƒ n\ d | | f } t d t | f d ƒ } | j | ƒ | j ƒ  d | GH| j | | d ƒ | } q< W| j ƒ  d  S(   Ni    t   spurpuratust   dbFilet   rt    t
   purpuratusi   iÿÿÿÿt   _t   >iPÃ  s   Added contig %s to databaset
   chromosomet   dbs   %s%s.bins   %s%st   ws    Added contig file %s to databaset   file(   R    t   opent   readlinet   splitt   stript   lent   appendt   stringt   joint   addSequencet   strt   addChromosomeEntryt   cisRoott   writet   close(   R   t	   chromPatht   chromOutPatht   seqArrayt   seqLent   spGenomet   inFilet   headert   fieldst   idpartt   partst   chromIDt   currentLinet   lineSeqt   seqt   outFileNamet   outFile(    (    sh   /woldlab/castor/data00/home/georgi/code/erange-4.0a-BAM-2014-05-09-fix/cistematic/genomes/spurpuratus.pyt   loadChromosome+   sB    
	"
	
c         C   s)   t  d d d d |  ƒ} | j |  ƒ d  S(   NR   t   versions   2.1R   (   R    t   createGeneDB(   R   R    (    (    sh   /woldlab/castor/data00/home/georgi/code/erange-4.0a-BAM-2014-05-09-fix/cistematic/genomes/spurpuratus.pyt   createDBFileU   s    c         C   s&   t  d d d d |  ƒ} | j ƒ  d  S(   NR   R-   s   2.1R   (   R    t   createIndices(   R   R    (    (    sh   /woldlab/castor/data00/home/georgi/code/erange-4.0a-BAM-2014-05-09-fix/cistematic/genomes/spurpuratus.pyt   createDBindicesZ   s    c         C   sT   d t  } d } d |  GHt |  ƒ d GHt |  | | ƒ d GHt |  ƒ d |  GHd  S(   Ns   %s/download/Spur2.1_Nmasked.txts   /S_purpuratus/s   Creating database %ss   Loading genomic sequences   Creating Indicess   Finished creating database %s(   R   R/   R,   R1   (   R   t
   chromoPatht   chromoOutPath(    (    sh   /woldlab/castor/data00/home/georgi/code/erange-4.0a-BAM-2014-05-09-fix/cistematic/genomes/spurpuratus.pyt   buildSpurpuratusDB_   s    
	

(   R   t   cistematic.genomesR    t   osR   t   getR   t   geneDBR,   R/   R1   R4   (    (    (    sh   /woldlab/castor/data00/home/georgi/code/erange-4.0a-BAM-2014-05-09-fix/cistematic/genomes/spurpuratus.pyt   <module>   s   
	*		