uMc@sddkZddkZddkZddkZddkZddkZddklZddklZddkl Z ddk Te Z ei ZdefdYZdZyeWn#ej odd klZnXd efd YZd efd YZdefdYZdefdYZdefdYZdefdYZdefdYZ e dZ!e"e dZ#e"dZ$e"e dZ%dS(iN(trandom(tizip(t itemgetter(t*t ParseErrorcBs#eZdZddZdZRS(s9Indicates that a file format is not to expectation. s Parsing ErrorcCs ||_dS(N(t parameter(tselftvalue((sO/woldlab/castor/data00/home/georgi/programs/block_bootstrap-0.8.1/base_types.pyt__init__scCs|iS(N(R(R((sO/woldlab/castor/data00/home/georgi/programs/block_bootstrap-0.8.1/base_types.pyt__str__s(t__name__t __module__t__doc__RR (((sO/woldlab/castor/data00/home/georgi/programs/block_bootstrap-0.8.1/base_types.pyRs cCs=ddk}|id|}||d|dGscCs|dS(i((R((sO/woldlab/castor/data00/home/georgi/programs/block_bootstrap-0.8.1/base_types.pyR HscCs|d|ddS(ii((R((sO/woldlab/castor/data00/home/georgi/programs/block_bootstrap-0.8.1/base_types.pyR IscCsgt|tptt|i|i}t|i|i}||jot||fSdSdS(sReturn the intersection of self and otherInt as a tuple of intervals. If the intersecton is empty, returns an empty tuple. N((RRtAssertionErrortmaxRtminR(Rt otherIntervalRR((sO/woldlab/castor/data00/home/georgi/programs/block_bootstrap-0.8.1/base_types.pyt intersectionKs  cCst|tpt|ip.|i|idjp|i|idjo;t|i|i}t|i|i}t||fS||fSdS(sLReturn the union of self and otherInterval as a tuple of intervals. iN(RRR!t does_overlapRRR#R"(RR$RR((sO/woldlab/castor/data00/home/georgi/programs/block_bootstrap-0.8.1/base_types.pytunionWs cCsNt|tpttt|d|dt|d|dddS(Nii(RRR!R"R#(RR$((sO/woldlab/castor/data00/home/georgi/programs/block_bootstrap-0.8.1/base_types.pytoverlapescCs*t|tpt|i|djS(Ni(RRR!R((Rtother((sO/woldlab/castor/data00/home/georgi/programs/block_bootstrap-0.8.1/base_types.pyR&iscCsbt|tttfo|i|jSt|tjo|i|ijStdt|dS(Ns4Can't compare an object of type %s to a slice object( RRRtfloatRRRRt TypeError(RR)((sO/woldlab/castor/data00/home/georgi/programs/block_bootstrap-0.8.1/base_types.pyt__lt__ns cCsbt|tttfo|i|jSt|tjo|i|ijStdt|dS(Ns4Can't compare an object of type %s to a slice object( RRRR*RRRRR+(RR)((sO/woldlab/castor/data00/home/georgi/programs/block_bootstrap-0.8.1/base_types.pyt__le__us cCs8t|ttttfptS||jo ||jS(N(RRRR*RtFalse(RR)((sO/woldlab/castor/data00/home/georgi/programs/block_bootstrap-0.8.1/base_types.pyt__eq__|scCs ||j S(N((RR)((sO/woldlab/castor/data00/home/georgi/programs/block_bootstrap-0.8.1/base_types.pyt__ne__scCsbt|tttfo|i|jSt|tjo|i|ijStdt|dS(Ns4Can't compare an object of type %s to a slice object( RRRR*RRRRR+(RR)((sO/woldlab/castor/data00/home/georgi/programs/block_bootstrap-0.8.1/base_types.pyt__ge__s cCsbt|tttfo|i|jSt|tjo|i|ijStdt|dS(Ns4Can't compare an object of type %s to a slice object( RRRR*RRRRR+(RR)((sO/woldlab/castor/data00/home/georgi/programs/block_bootstrap-0.8.1/base_types.pyt__gt__s (R R R t __slots__RtpropertyRRtsizeR%R'R(R&R,R-R/R0R1R2(((sO/woldlab/castor/data00/home/georgi/programs/block_bootstrap-0.8.1/base_types.pyR,s          tregioncBseZdddddZdZdZeeeZdZddZ dZ ee Z e dZ dZd Zd Zd Zd Zd ZdZdZdZdZdZdZdZdZgdZdZdZRS(cCsBg|_ti|i|ti||||_||_dS(N(tvaluestlistRtnamet_length(Rtintervals_itert values_iterR9tlength((sO/woldlab/castor/data00/home/georgi/programs/block_bootstrap-0.8.1/base_types.pyRs   cCsXt|tptt|djo!||dijo tdn||_dS(Niis3All bp indices must be less than the region length.(RRR!tlenRRR:(Rt new_length((sO/woldlab/castor/data00/home/georgi/programs/block_bootstrap-0.8.1/base_types.pyt _set_lengths' cCs|iS(N(R:(R((sO/woldlab/castor/data00/home/georgi/programs/block_bootstrap-0.8.1/base_types.pyt _get_lengthscCspg}g}t|i||i}t|i||di}||djoF||i|ijo/||i|ijo|i|c|7tappendRtinserttpdbt set_tracetreversedtzip(RRRtnewt new_valuet new_intervalst new_valueststart_bptend_bpt old_intervalst_[1]t old_intervaltold_interval_startst_[2]told_interval_endstindexRItitemR((sO/woldlab/castor/data00/home/georgi/programs/block_bootstrap-0.8.1/base_types.pyt_merge_intervalssV($$*$$!!     icCs |idjo |i|ijo tdnt|djp$t|djo5||djo$ti|||ii|n|ti ||}||i |o,ti ||}|i ||||n*ti |||ti |i||dS(Ns+All bps must be less than the region lengthii(R=tNoneRRR>R8RGR7tbisectt bisect_leftR&t bisect_rightR[RH(Rtcoverage_regionRtl_loctr_loc((sO/woldlab/castor/data00/home/georgi/programs/block_bootstrap-0.8.1/base_types.pytadds# 7cCs t|S(N(R>(R((sO/woldlab/castor/data00/home/georgi/programs/block_bootstrap-0.8.1/base_types.pyt _numRegionssc sdjo djpt|o ndti|}ti|}|t||}t|dfd|iDdt|i||!d|i dS(s1Return a copy of the genomic subregion. iR;c3sBx;|]4}tt|it|iVqWdS(N(RR"RR#R(t.0RZ(t shift_valuetstop_bpRQ(sO/woldlab/castor/data00/home/georgi/programs/block_bootstrap-0.8.1/base_types.pys s R<R9R=( R!R]R^R_RDRtiter_feature_regionstiterR7R9(RRQRgt shift_to_zerot start_indext stop_indext intervals((RfRgRQsO/woldlab/castor/data00/home/georgi/programs/block_bootstrap-0.8.1/base_types.pyt get_subregion s!  c Csti||i}ti||i}|t||}||jo d}n!||di||id}t|dd|iDdt|i ||!d|i d|S(sHReturn a copy of the genomic subregion that overlaps interval. iiR;css(x!|]}t|i|iVqWdS(N(RRR(ReRZ((sO/woldlab/castor/data00/home/georgi/programs/block_bootstrap-0.8.1/base_types.pys 0s R<R9R=( R]R^RR_RRDRRhRiR7R9(RtinterRkRlR=((sO/woldlab/castor/data00/home/georgi/programs/block_bootstrap-0.8.1/base_types.pytget_overlapping_intervals!s    cCsPy)ddk}|it|iSWn tj ot|iSXdS(ssReturn a numpy array of all scores. If numpy is not available, return a list of scores. iN(tnumpytarrayR8t iter_featurest ImportError(RRq((sO/woldlab/castor/data00/home/georgi/programs/block_bootstrap-0.8.1/base_types.pytbp_score_array7s  cCsEd}x+|iD]\}}||i|7}qWt||iS(s%Return the mean of all values in selfi(titer_intervals_and_valuesR5R*R=(RtrvRZR((sO/woldlab/castor/data00/home/georgi/programs/block_bootstrap-0.8.1/base_types.pytmeanCs  cCs|i}d}d}x@|iD]2\}}||i7}||i||d7}q%W||i||d7}t||idS(s2Return the centered variance of all values in selfiii(RxRvR5R=R*(RRxtret_valt total_sizeRZR((sO/woldlab/castor/data00/home/georgi/programs/block_bootstrap-0.8.1/base_types.pytvarJs   c Cs<t|djpt|djotGdGHdStdnd}d}|i}|i}y&ddk}t||i}WnStj oGtg}t||D]\}} |t|| q~}nX||i|i |i } | |idt i |i t i |i } | S(s=Return the pearson correlation of self and other, by basepairis/Can't take the correlation of a 0 length vectorgiNi( R>RRuRqR*tsumRtRR=RxtmathtsqrtR{( Rt otherRegiontoverlapProductt other_indextd1td2RqRTti1ti2tp_corr((sO/woldlab/castor/data00/home/georgi/programs/block_bootstrap-0.8.1/base_types.pytregionCorrelationUs &     E!7ccs7x0tt|D]}|||i|fVqWdS(N(RFR>R7(RRY((sO/woldlab/castor/data00/home/georgi/programs/block_bootstrap-0.8.1/base_types.pyRvsc cs x!t|ddD] }dVqWxtt|dD]n}|i|}x t||iD] }|VqbWx5t||dd||ddD] }dVqWq;W|id}x t|diD] }|VqWx(t|i|ddD] }dVqWdS(sIterates through every feature in the interval. For instance, if the region was of length 10 and had a single feature interval [2,8] this would return 0 0 1 1 1 1 1 1 1 0. iiiN(RFR>R7R5R=(RtloopRtiloop((sO/woldlab/castor/data00/home/georgi/programs/block_bootstrap-0.8.1/base_types.pyRss(   )    cCs.tg}|iD]}||iq~S(N(R|RhR5(RRTtfeature((sO/woldlab/castor/data00/home/georgi/programs/block_bootstrap-0.8.1/base_types.pytfeaturesLengthsccs#xti|D] }|VqWdS(sIterates through every feature region in the interval. For instance, if the region was of length 10 and had a single feature interval [2,8] this would return interval(2, 8). N(R8t__iter__(Rtfeature_interval((sO/woldlab/castor/data00/home/georgi/programs/block_bootstrap-0.8.1/base_types.pyRhs cCs tddS(syMake sure that we arent using iter incorrectly. If you want the list iterator call list.__iter__(self). sXNo defined iterator - call the particular fn directly ( ie iter_feature_regions, etc. ).N(tNotImplementedError(R((sO/woldlab/castor/data00/home/georgi/programs/block_bootstrap-0.8.1/base_types.pyRscCs5t}t|djo|||i<|S|idjo d}n|id}tti|}|idd|i|ixwt dt|dD]\}|i ||||dt ||d|d<|d|d||d|d_qW|it d|i Djpt|S(s;Splits this region into a regions object. itt_issplit_%icssx|]}|iVqWdS(N(R=(ReRZ((sO/woldlab/castor/data00/home/georgi/programs/block_bootstrap-0.8.1/base_types.pys s N(tregionsR>R9R\R8tcopyRHRGR=RFRntTrueR|R7R!(Rt split_pointsRwR9RY((sO/woldlab/castor/data00/home/georgi/programs/block_bootstrap-0.8.1/base_types.pyRs     1)-cCs|it||dS(N(RCRDR\(RRtstop((sO/woldlab/castor/data00/home/georgi/programs/block_bootstrap-0.8.1/base_types.pyt __getslice__scCs~t|tjoti||St|tjptt|tti||tti|i||iS(N( RRR8RCRDR!RiR7R9(RRB((sO/woldlab/castor/data00/home/georgi/programs/block_bootstrap-0.8.1/base_types.pyRCs cCsttdd|i|i}d}xL|iD]>\}}|i|||||if|||i7}q.W|S(slReturn a copy of this region in cumulative space. 1,1,1,2,2,2 becomes 1,2,3,5,7,9 i(((t cum_regionR9R=RvRcR5(Rt new_regiont curr_valueRR((sO/woldlab/castor/data00/home/georgi/programs/block_bootstrap-0.8.1/base_types.pyt build_cdfs !cCsddk}g}|id|iD] }||q&~}|i|ig}|D]}||i|qW~}|i||x|D]}|i|qW|idS(Nii(tpylabtiter_split_pointsR=RGRtplottaxvlinetshow(RRRRTtentrytpointsRWR7((sO/woldlab/castor/data00/home/georgi/programs/block_bootstrap-0.8.1/base_types.pyRs 0*ccsti|}|i}x!|i|jo|i}qWx]|id|joH|idV|idjo|i|jo |iVn|i}qBWdS(Ni(R8RtnextRRR5(RtminValuetmaxValuetiteratorR((sO/woldlab/castor/data00/home/georgi/programs/block_bootstrap-0.8.1/base_types.pyR s    cCswt|ttfptti||}|djodS||di}||jodS|i|dSdS(s2Return the value at a specific basepair. iiN(RRRR!R]R_RR7(Rtbp_indextr_indextprev_interval_start((sO/woldlab/castor/data00/home/georgi/programs/block_bootstrap-0.8.1/base_types.pyRs  ((N(R R R\RR@RAR4R=R[RcRdt numRegionsR.RnRpRuRxR{RRvRsRRhRRRRCRRRR(((sO/woldlab/castor/data00/home/georgi/programs/block_bootstrap-0.8.1/base_types.pyR6s4   I       /     &  RcBs)eZdZdZdZdZRS(sStore region data as a frozen cumulative sum. The 'value' at a bp is the sum of the values *up to and including* that bp. Also, the object is frozen, making way for future optimization. cGs tddS(Ns-'cum_region' object has no attribute 'append'(tAttributeError(Rtargs((sO/woldlab/castor/data00/home/georgi/programs/block_bootstrap-0.8.1/base_types.pyRG3scGs tddS(Ns4'cum_region' object does not support item assignment(R+(RR((sO/woldlab/castor/data00/home/georgi/programs/block_bootstrap-0.8.1/base_types.pyt __setitem__6scCst|ttfptti||}|djodS||di}||jo|i|ddS|i|dd|i|dd||di}|i|dd||||di dSdS(s2Return the value at a specific basepair. iiN( RRRR!R]R_RR7R5R(RRRRt per_bp_factor((sO/woldlab/castor/data00/home/georgi/programs/block_bootstrap-0.8.1/base_types.pyR9s  7(R R R RGRR(((sO/woldlab/castor/data00/home/georgi/programs/block_bootstrap-0.8.1/base_types.pyR,s  t binary_regioncBsweZdZdZd d d ddZdZdZdZddZ dZ d Z d Z d Z RS(s<A region object optimized to work with binary regions. cCsti||ddS(Ni(R6Rc(RR((sO/woldlab/castor/data00/home/georgi/programs/block_bootstrap-0.8.1/base_types.pyRcWscCsti||d||dS(N((R6R(RR;R9R=R<((sO/woldlab/castor/data00/home/georgi/programs/block_bootstrap-0.8.1/base_types.pyRZsc Cs|||}}}tt||i|it||di|i}toto/d|||fGHdGHd|||fGHnxCt|d|dD]+} todt|| GHn|| =qWto dGHqn|||RhRRRR\RGt StopIterationR((Rt otherAnnTrackt totalOverlaptcurrentMatchestthisItert nextMatchtivRZ((sO/woldlab/castor/data00/home/georgi/programs/block_bootstrap-0.8.1/base_types.pyR(vs0&      cCst|djpt|djodS|i|ijptd|i|ifn|i}|i|}|i}|i}||||ti||ti|dti||ti|d}|S(sG Calculate the correlation of this region with another region isBCan't calculate correlation of regions of unequal length: (%i, %i)i(R>R=RR(RR}R~tpow(RRtnR(tbp1tbp2tcorr((sO/woldlab/castor/data00/home/georgi/programs/block_bootstrap-0.8.1/base_types.pyRs&   TgcCst|djodSd}d}d}xti|D]}x9|t|jo%||i|ijo|d7}qCW|t|joPn|i||}|djoG|||ijo3||||i|||if|d7}q:q:q:W|S(sCalculate the number of regions that overlap self with the given region We take self to be the covered region. ie, for self =============================== other --- ---- ----------- - the region overlap is 1, whereas for self =========== ================== other --- ---- ----------- - it is 2. The algorithm is nearly identical to they overlap fn - it's a merge join ii(R>R8RRRR(R5(RRtmin_coverage_percentRt self_indexRRR(((sO/woldlab/castor/data00/home/georgi/programs/block_bootstrap-0.8.1/base_types.pyt regionOverlaps(!  cCs?d}x2|D]*}x!|D]}||i|7}qWq W|S(Ni(R((RRRtother_ivtself_iv((sO/woldlab/castor/data00/home/georgi/programs/block_bootstrap-0.8.1/base_types.pyt bruteOverlapscCs]d}xPti|D]?}x6ti|D]%}|i|o|d7}Pq,q,WqW|S(Nii(R8RR&(RRRRR((sO/woldlab/castor/data00/home/georgi/programs/block_bootstrap-0.8.1/base_types.pytbrute_regionOverlaps  ccs0x)tt|D]}||dfVqWdS(Ni(RFR>(RRY((sO/woldlab/castor/data00/home/georgi/programs/block_bootstrap-0.8.1/base_types.pyRvsc csx!t|ddD] }dVqWxtt|dD]j}x-t||d||dD] }dVqbWx1t||dd||dD] }dVqWq;Wx-t|dd|ddD] }dVqWx(t|i|ddD] }dVqWdS(s)Iterates through every feature in the interval. Overrides the iter_features for region class and applies to binary regions For instance, if the region was of length 10 and had a single feature interval [2,8] this would return 0 0 1 1 1 1 1 1 1 0. iiiN(RFR>R=(RRR((sO/woldlab/castor/data00/home/georgi/programs/block_bootstrap-0.8.1/base_types.pyRss$  ! % !  (N((R R R RcR\RR[R(RRRRRvRs(((sO/woldlab/castor/data00/home/georgi/programs/block_bootstrap-0.8.1/base_types.pyRSs     . tgenomic_coverage_regioncBs/eZdZeeZdZdZRS(cCs[y |iSWnFtj o:tg}|iD]}||iq0~|_nX|iS(N(t_cached_lengthRR|RhR5(RRTR((sO/woldlab/castor/data00/home/georgi/programs/block_bootstrap-0.8.1/base_types.pyR: s  8cCs.t|do |`nti||dS(NR(thasattrRR6RG(RR((sO/woldlab/castor/data00/home/georgi/programs/block_bootstrap-0.8.1/base_types.pyRGs cCsNti||i}ti||i}||jodSt|djpt|di|ijpt|di|ijpttg}t i |D]}||i |q~}|djo|d|!i }nd}|i||ijo||i||i7}n|djptt |||dS(s|Return the intersection of inter and self, *in genomic coordinates* inter needs to be an interval. iiiN(R]R^RR_RR\R>R!R|R8RR(R=R(RRoRaRbRTRZt bp_overlapt new_start((sO/woldlab/castor/data00/home/georgi/programs/block_bootstrap-0.8.1/base_types.pyR%s 9 (R R R:R4R=RGR%(((sO/woldlab/castor/data00/home/georgi/programs/block_bootstrap-0.8.1/base_types.pyR s   RcBsGeZdZdZeeZdZdZdZdZ RS(sA region container object. This is just a dictionary of region's whereby each key is the region's track name. Also contains a method to store an overlap stat. cCsby |iSWnPtj oDttg}|iD]}||iq3~|_|iSXdS(s@Calculate the total length and cache it for later use. N(t_cached_totalLengthRR*R|R7R=(RRTR((sO/woldlab/castor/data00/home/georgi/programs/block_bootstrap-0.8.1/base_types.pyt _totalLengthKs  9cCsGtg}|iD])\}}||t|i|ifq~S(sReturns a dict of the relative region lengths. For instance, if there are two regions of names R1 and R2 and they are both the same length then this will return { 'R1': 0.5, 'R2': 0.5 } (tdictt iteritemsR*R=t totalLength(RRTRBR((sO/woldlab/castor/data00/home/georgi/programs/block_bootstrap-0.8.1/base_types.pytregionFractionVscCssxL|iD]>}|i|otd|||fn||||Can not extend %r with %r: they both contain a region named %s(tkeysthas_keyRRR(RR)RB((sO/woldlab/castor/data00/home/georgi/programs/block_bootstrap-0.8.1/base_types.pytextend`s  cCs|i}|ixm|D]e}x>||iD],\\}}}|id|||fq4W|id|||ifqWdS(Ns %s %i %i s%s 0 %i (RRERvtwriteR=(Rtbed_ft lengths_fRRBRRR((sO/woldlab/castor/data00/home/georgi/programs/block_bootstrap-0.8.1/base_types.pyt writeBedFilems  cCs|i}|ix|D]}xt||iD]\}\\}}}t||toU|idit|ddt|t|ddddt|f dq:|idit|ddt|t|t|dddt|f dq:WqWdS(Ns tmerged_featuret.sID=s ( RREt enumerateRvRRRRR(Rtgff3_fRRBtiRRR((sO/woldlab/castor/data00/home/georgi/programs/block_bootstrap-0.8.1/base_types.pyt writeGff3Filews  U( R R R RR4RRRRR(((sO/woldlab/castor/data00/home/georgi/programs/block_bootstrap-0.8.1/base_types.pyRAs  tlazy_wiggle_filecBs;eZdZdZdZdZdZdZRS(sA memory safe wiggle parser. We region subselects that are done on disk to increase access efficiency when the entire file is too big to fit in memory. cCsfddk}|i}x1|id}|djoPn|i|q|iid|iS(sReturn the hex digest of a file without loading it all into memory This caches the data structure and checks that it hasnt changed.iNiRi(tmd5RMtreadtupdatetftseekt hexdigest(RtfhRtdigesttbuf((sO/woldlab/castor/data00/home/georgi/programs/block_bootstrap-0.8.1/base_types.pytmd5files   c svd}fd}iidd}d}d}ii}x |djo|idohii}ii}x@|ido/|djo"ii}ii}qWqLn|idp|idoed}|djo||n|||}|}|d djo|d |d |d s cssx|]}|dVqWdS(RN((ReR7((sO/woldlab/castor/data00/home/georgi/programs/block_bootstrap-0.8.1/base_types.pys s RRRRRRRRRs\s+RiN(((R\RR"R6RRRRR!RtstripRRR*RcRRn(Rtchr_nameRQRgRRTR7t all_valuestsub_region_lengtht sub_regionRt search_locRtf_loctposttmp_posR((sO/woldlab/castor/data00/home/georgi/programs/block_bootstrap-0.8.1/base_types.pyRnsL6%'       1 cCstddk}ddk}d|_t|_t|ttfot|_ t ||_ nt |_ ||_ |i |i |_d|i i}|ii|oh|ii|oUt |d}|i||_|i|iijot|_n|int|idjoI|i|i|i_t |d}|i|i||indS(Nii's.cached_annotation_pntstrbitwb(tcPickletosRtsc_dictRRRtunicodeRtopened_ftopenRR.Rtmd5sumR9tpathtexiststisfiletloadtcloseR>Rtdump(Rtwig_fRRtfnameR((sO/woldlab/castor/data00/home/georgi/programs/block_bootstrap-0.8.1/base_types.pyR-s,     & cCs t|iS(N(RR(R((sO/woldlab/castor/data00/home/georgi/programs/block_bootstrap-0.8.1/base_types.pyR Ps(R R R RRRnRR (((sO/woldlab/castor/data00/home/georgi/programs/block_bootstrap-0.8.1/base_types.pyRs   [ : #c Cs|idt}xt|D]\}}tid|i}t|djo*td|d|i|ifn|dd!\}}} t t |t | } |i |pt d|||RR9RRRRRGRR=RR6R\RRRRRRRt IndexErrorRtmapR*Rc(Rt lengths_filetBINARYtlengthstline_numRR7tchNameRRRt chromosomesR=tcurr_chrt curr_spantlast_posR R((sO/woldlab/castor/data00/home/georgi/programs/block_bootstrap-0.8.1/base_types.pytparse_wiggle_fileSs   *             !   -1cCsBddk}t}xt|D]\}}|id|i}t|djo*td|d|i|ifn|dd!\} } } tt | t | } |i | pt d| || RR9RRRRRGRR=RR6RR\RR%RcRR*R(RR!tgroupt is_binaryRR#R$RR7R%RRRR&R=R9tshifted_featureR((sO/woldlab/castor/data00/home/georgi/programs/block_bootstrap-0.8.1/base_types.pytparse_bed_line_iteratorsv   $           cs1fd}t||d|dt}|S(Nc3sfx_D]W}|idoqndidttid|iDd}|VqWdS(NRs css0x)|]"\}}|djo |VqqWdS(iiiN(iii((ReRRZ((sO/woldlab/castor/data00/home/georgi/programs/block_bootstrap-0.8.1/base_types.pys s s\s+s (RRRRRR(Rt this_line(R(sO/woldlab/castor/data00/home/georgi/programs/block_bootstrap-0.8.1/base_types.pytiter_gffslines_as_bedliness "R+R,(R.R(RR!R+R0t projected_bed((RsO/woldlab/castor/data00/home/georgi/programs/block_bootstrap-0.8.1/base_types.pytparse_gff3_files cCsddk}|id|id|id|ii}t|djo1tiddi|IJt d|i n+t|djp|o t }nt }|idt ||||}|S( sParse a bed and lengths file into a regions object. If group is specified, only BED lines whose "name" line matches group are added to the regions object iNis\s+isOffending values: '%s' s s0Error parsing "%s": this is not a valid BED file(RRRRRR>tsyststderrRRR9RR.R.(RR!R+t force_binaryRR7R"R&((sO/woldlab/castor/data00/home/georgi/programs/block_bootstrap-0.8.1/base_types.pytparse_bed_files     (&R3R}toperatorR]RRRt itertoolsRRtstatistical_functionsR.Rtstdouttoutputt ExceptionRRtsett NameErrortsetsRRRR8R6RRRRRtobjectRR*R\R.R2R6(((sO/woldlab/castor/data00/home/georgi/programs/block_bootstrap-0.8.1/base_types.pyts:         f'6B [W