Ñò Xs*Jc @sÃdZddkZddkZddkZddkZddkZddkTddkTeidƒZ eidƒZ ddk Z dZ dd d„ƒYZ d dd „ƒYZd dd „ƒYZdS(sE This module contains the classes to deal with UCSC known gene files iÿÿÿÿN(t*s\+s\-sError in UCSC classtUCSCcBs)eZdZd„Zd„Zd„ZRS(s¼ Class for keeping known gene information. This might be too much information to carry around when the most usefull parts are really the chrom, strand, txStart and txEnd. c Cs^||_||_||_||_||_||_||_||_| |_| |_ dS(N( tnametchromtstrandttxStartttxEndtcdsStarttcdsEndt exonCountt exonStartstexonEnds( tselfRRRRRRRR R R ((s@/woldlab/castor/data00/home/georgi/SICER_v1.01/SICER/lib/UCSC.pyt__init__,s         c Cs^||_||_||_||_||_||_||_||_| |_| |_ dS(N( RRRRRRRR R R ( R RRRRRRRR R R ((s@/woldlab/castor/data00/home/georgi/SICER_v1.01/SICER/lib/UCSC.pyt__set__9s         cCsÁ|id|id|idt|iƒdt|iƒdt|iƒdt|iƒdt|iƒdt|i ƒdt|i ƒ}y|SWnt i i d|ƒdSXdS(Nt s&No UCSC known gene information for %s t(RRRtstrRRRRR R R tsyststderrtwrite(R t outstring((s@/woldlab/castor/data00/home/georgi/SICER_v1.01/SICER/lib/UCSC.pytgetAllFs –(t__name__t __module__t__doc__R RR(((s@/woldlab/castor/data00/home/georgi/SICER_v1.01/SICER/lib/UCSC.pyR%s t UCSC_litecBs)eZdZd„Zd„Zd„ZRS(sh Class for keeping known gene information. Only partial (most usefull) information stored. cCs1||_||_||_||_||_dS(N(RRRRR(R RRRRR((s@/woldlab/castor/data00/home/georgi/SICER_v1.01/SICER/lib/UCSC.pyR [s     cCs1||_||_||_||_||_dS(N(RRRRR(R RRRRR((s@/woldlab/castor/data00/home/georgi/SICER_v1.01/SICER/lib/UCSC.pyRas     cCsl|id|id|idt|iƒdt|iƒ}y|SWntiid|ƒdSXdS(NRs&No UCSC known gene information for %s R( RRRRRRRRR(R R((s@/woldlab/castor/data00/home/georgi/SICER_v1.01/SICER/lib/UCSC.pyRhs A(RRRR RR(((s@/woldlab/castor/data00/home/georgi/SICER_v1.01/SICER/lib/UCSC.pyRVs  t KnownGenescBsteZdZd d„Zd„Zd„Zd„Zd„Zd„Z d„Z d„Z d „Z d „Z d „ZRS( sE Class to read in UCSC known gene files and get all the info c Cs h|_t|ƒ}xñ|D]é}tid|ƒpÐ|iƒ}|iƒ}|d|iiƒjog|i|dR@RBRDRERF(((s@/woldlab/castor/data00/home/georgi/SICER_v1.01/SICER/lib/UCSC.pyRvs        ((((RRtostshutilttimeRtmathtstringtcompileR,R-tBEDR=RRR(((s@/woldlab/castor/data00/home/georgi/SICER_v1.01/SICER/lib/UCSC.pyts<   1