Ñò lV.Jc @sédZddkZddkZddkZddkZddkZddkTddkTddkZei dƒZ ei dƒZ dZ ddd„ƒYZ d dd „ƒYZd dd „ƒYZd dd„ƒYZddd„ƒYZdS(s= This module contains all the classes to deal with BED files iÿÿÿÿN(t*s\+s\-sError in BED classtBED2cBs)eZdZd„Zd„Zd„ZRS(sÀ Class for bed lines with 2 values: start and strand, this will be useful for things like TSS information or tags where the only important information is the start and strand. cCs||_||_dS(N(tstarttstrand(tselfRR((s?/woldlab/castor/data00/home/georgi/SICER_v1.01/SICER/lib/BED.pyt__init__8s cCs||_||_dS(N(RR(RRR((s?/woldlab/castor/data00/home/georgi/SICER_v1.01/SICER/lib/BED.pyt__set__<s cCsEt|iƒd|i}y|SWntiid|ƒdSXdS(Nt sNo coord information for %s t(tstrRRtsyststderrtwrite(Rt outstring((s?/woldlab/castor/data00/home/georgi/SICER_v1.01/SICER/lib/BED.pytgetCoord@s (t__name__t __module__t__doc__RRR(((s?/woldlab/castor/data00/home/georgi/SICER_v1.01/SICER/lib/BED.pyR2s  tBED3cBs)eZdZd„Zd„Zd„ZRS(sA Class for bed lines with 3 values: chrom, start and end cCs||_||_||_dS(N(tchromRtend(RRRR((s?/woldlab/castor/data00/home/georgi/SICER_v1.01/SICER/lib/BED.pyRPs  cCs||_||_||_dS(N(RRR(RRRR((s?/woldlab/castor/data00/home/georgi/SICER_v1.01/SICER/lib/BED.pyRVs  cCsV|idt|iƒdt|iƒ}y|SWntiid|ƒdSXdS(NRsNo coord information for %s R(RR RRR R R (RR ((s?/woldlab/castor/data00/home/georgi/SICER_v1.01/SICER/lib/BED.pyR\s +(RRRRRR(((s?/woldlab/castor/data00/home/georgi/SICER_v1.01/SICER/lib/BED.pyRLs  tBED6cBs)eZdZd„Zd„Zd„ZRS(sT Class for bed lines with 6 values: chrom, start, end, name, score, strand cCs:||_||_||_||_||_||_dS(N(RRRtnametscoreR(RRRRRRR((s?/woldlab/castor/data00/home/georgi/SICER_v1.01/SICER/lib/BED.pyRns      cCs:||_||_||_||_||_||_dS(N(RRRRRR(RRRRRRR((s?/woldlab/castor/data00/home/georgi/SICER_v1.01/SICER/lib/BED.pyRvs      cCs}|idt|iƒdt|iƒd|idt|iƒd|i}y|SWntii d|ƒdSXdS(Ns sNo coord information for %s R( RR RRRRRR R R (RR ((s?/woldlab/castor/data00/home/georgi/SICER_v1.01/SICER/lib/BED.pyR~s R(RRRRRR(((s?/woldlab/castor/data00/home/georgi/SICER_v1.01/SICER/lib/BED.pyRis  t BED_GRAPHcBs5eZdZdd„Zd„Zd„Zd„ZRS(sk Class to deal with bed graph lines: chrom, start, end, value This emulates the wiggle format icCs(||_||_||_||_dS(N(RRRtvalue(RRRRR((s?/woldlab/castor/data00/home/georgi/SICER_v1.01/SICER/lib/BED.pyR’s   cCs(||_||_||_||_dS(N(RRRR(RRRRR((s?/woldlab/castor/data00/home/georgi/SICER_v1.01/SICER/lib/BED.pyR—s   cCsV|idt|iƒdt|iƒ}y|SWntiid|ƒdSXdS(NRs No BED coord information for %s R(RR RRR R R (RR ((s?/woldlab/castor/data00/home/georgi/SICER_v1.01/SICER/lib/BED.pyRœs +cCsg|idt|iƒdt|iƒdt|iƒ}y|SWntiid|ƒdSXdS(NRsNo BED all information for %s R(RR RRRR R R (RR ((s?/woldlab/castor/data00/home/georgi/SICER_v1.01/SICER/lib/BED.pytgetAll£s <(RRRRRRR(((s?/woldlab/castor/data00/home/georgi/SICER_v1.01/SICER/lib/BED.pyRŒs    tBEDcBs¡eZdZddddd„Zd„Zd„Zd„Zd„Zd „Z d „Z d „Z d „Z d „Z d„Zd„Zd„Zd„Zd„ZRS(s@ Class to deal with bed files and do common operations thg18Ric Cs0h|_x"ti|D]}g|i|R@RCRERGRIRJRKRMRN(((s?/woldlab/castor/data00/home/georgi/SICER_v1.01/SICER/lib/BED.pyR¯s o        ((((((RR!tostshutilttimeR tmathtstringRtcompileR+R,R*RRRRR(((s?/woldlab/castor/data00/home/georgi/SICER_v1.01/SICER/lib/BED.pyts<   ##