ó ” iHc@s›ddlZddlZddlZddlTdefd„ƒYZd„Zedkr—e ej ƒdkrƒdGHej d ƒneej d ƒndS( iÿÿÿÿN(t*tBedcBsAeZdZd„Zd„Zdd„Zd„Zdd„ZRS(s Bed file object 1) if the bed file is not very large: bed1 = Bed() bed1.readbed(bedfilename) bed1.bedsort() bed1.release_space() 2) if the bed file is very large: bed1 = Bed() bed1.bedsort_by_chr(bedfilename) bed1.release_space() cCs:g|_g|_g|_g|_g|_d|_dS(N(tchromstchrtbegintendtcontenttNonet bedfilename(tself((s</woldlab/castor/data00/home/georgi/programs/NPS-1.3.2/Bed.pyt__init__s      cCsQ||_x»t|ƒjƒD]§}|d dkr|jƒjƒ}|jj|dƒ|d|jkr‚|jj|dƒn|jj|dƒ|j j|dƒ|j j|jƒƒqqWt j |jƒ|_t g|jD]}t |ƒ^qétƒ|_t g|j D]}t |ƒ^qtƒ|_ t j |j ƒ|_ dS(s3readbed(bedfilename) read bed file iRiiiN(Rtopent xreadlineststriptsplitRtappendRRRRtchartarraytinttint32(R Rtlineoldtlineti((s</woldlab/castor/data00/home/georgi/programs/NPS-1.3.2/Bed.pytreadbeds ..tc Cs?|jjtƒ|r|}nu|jjdƒ}t|ƒdkrgdj|dd|dgƒ}n-djdj|dd!ƒd|dgƒ}t|dƒ}x•tt|jƒƒD]~}t |j |j|kƒd}|j |}|j |}|j ds q¹n|jƒ} x| D]} ||| IJqWq¹W|S(sdbedsort(newfilename = '') The default new file name is self.bedfilename + '.sorted' t.iit_sortediiÿÿÿÿtw(RtsorttcmpRRtlentjoinR txrangetwhereRRRtshapetargsort( R tnewfiletofntlt outputfiletktsegmenttchrbegint chrcontenttindexR((s</woldlab/castor/data00/home/georgi/programs/NPS-1.3.2/Bed.pytbedsort/s$ $-      cCs:g|_g|_g|_g|_g|_d|_dS(s3release_space() release the memory N(RRRRRRR(R ((s</woldlab/castor/data00/home/georgi/programs/NPS-1.3.2/Bed.pyt release_spaceMs      cCss||_|r|}nu|jjdƒ}t|ƒdkr`dj|dd|dgƒ}n-djdj|dd!ƒd|dgƒ}t|dƒ}d}g|_g|_g|_g|_g|_ t j d It j ƒIJi}i}xŸt|ƒjƒD]‹} | d d kr| jƒ} | jƒ} || dkr¤|j| dƒsid|| d10G), the program cann't sort the bed file. Users can try other ways to sort the bed file. If the size is larger than 0.5G, the program use chr by chr sort instead of sorting all chr regions together. Iä Ts#The file is too large to be sorted!iieÍsSorting bed file ....s Start time:s End time:( R8R9tgetsizeR3R4texitR5R6RRR-R.RF(RtfilesizetbedR%RC((s</woldlab/castor/data00/home/georgi/programs/NPS-1.3.2/Bed.pytsortBed»s$          t__main__isUsage: %prog bedfileii( R3tos.pathR8R5tnumpytobjectRRNRGRtargvRK(((s</woldlab/castor/data00/home/georgi/programs/NPS-1.3.2/Bed.pyts$ ´