ó ?îec@s½dZddlZddlZddlmZmZddlmZddl m Z ddl m Z m Z ddlmZdefd „ƒYZd dd „ƒYZd efd „ƒYZdS(sv Script with classes and functions for nucleosome calling. @author: Alicia Schep, Greenleaf Lab, Stanford University iÿÿÿÿN(tTracktInsertionTrack(tChunk(tread_chrom_sizes_from_fasta(tPWMtInsertionBiasTrack(tcopytNFRcBs)eZdZd„Zd„Zd„ZRS(s7Class for storing information about a single NFR regioncCsµ|j|_||_||_d|_tj|jj||ƒƒ|_tj|j j||ƒƒ|_ tj|j j||ƒƒ|_ tj|j j||dtƒƒ|_dS(Nt*tlog(tchromtstarttendtstrandtnptmeantocctgettmint occ_uppert min_uppertinst ins_densitytbiastFalset bias_density(tselftlefttrighttnfrtrack((s;/tmp/pip-install-bGcd2k/NucleoATAC/nucleoatac/NFRCalling.pyt__init__s    !!!c CsFdjtt|j|j|j|j|j|j|j gƒƒ}|S(Ns ( tjointmaptstrR R R RRRR(Rtout((s;/tmp/pip-install-bGcd2k/NucleoATAC/nucleoatac/NFRCalling.pytasBedsBcCs|j|jƒdƒdS(Ns (twriteR#(Rthandle((s;/tmp/pip-install-bGcd2k/NucleoATAC/nucleoatac/NFRCalling.pyR$s(t__name__t __module__t__doc__RR#R$(((s;/tmp/pip-install-bGcd2k/NucleoATAC/nucleoatac/NFRCalling.pyRs t NFRParameterscBs)eZdZddddddd„ZRS(s:Class for storing parameters related to nucleosome callinggÐ?c Css||_||_||_||_||_||_||_|dk rotj |ƒ|_ t |ƒ|_ ndS(N( tbamt ins_trackt occ_tracktcallstmax_occt max_occ_uppertfastatNoneRtopentpwmRtchrs( RR,R-R+R*R.R/R0R3((s;/tmp/pip-install-bGcd2k/NucleoATAC/nucleoatac/NFRCalling.pyR$s        N(R&R'R(R1R(((s;/tmp/pip-install-bGcd2k/NucleoATAC/nucleoatac/NFRCalling.pyR)"stNFRChunkcBsVeZdZd„Zd„Zd„Zd„Zd„Zd„Zd„Z d„Z RS( sBClass for storing and determining collection of nfr positions cCs1|j|_|j|_|j|_g|_dS(N(R R R tnfrs(Rtchunk((s;/tmp/pip-install-bGcd2k/NucleoATAC/nucleoatac/NFRCalling.pyR5s   cCs ||_dS(N(tparams(Rt parameters((s;/tmp/pip-install-bGcd2k/NucleoATAC/nucleoatac/NFRCalling.pyt initialize:scCs€t|j|j|jdƒ|_|jj|jjƒ|jjd d}t|j|j|jdƒ|_|jj|ƒdS(s-gets occupancy track-- reads in from bedgrapht Occupancyiõÿÿÿsupper_bound.bedgraph.gzN( RR R R Rt read_trackR8R,R(Rt upper_file((s;/tmp/pip-install-bGcd2k/NucleoATAC/nucleoatac/NFRCalling.pytgetOcc<s !!cCs„|jjdkrIt|j|j|jƒ|_|jj|jj ƒn7t |j|j|jdƒ|_|jj |jjƒdS(s-gets insertion track-- reads in from bedgrapht InsertionN( R8R+R1RR R R RtcalculateInsertionsR*RR<(R((s;/tmp/pip-install-bGcd2k/NucleoATAC/nucleoatac/NFRCalling.pytgetInsFs !cCset|j|j|jdtƒ|_|jjdk ra|jj |jj|jj |jj ƒndS(sget biasR N( RR R R tTrueRR8R0R1t computeBiasR4R3(R((s;/tmp/pip-install-bGcd2k/NucleoATAC/nucleoatac/NFRCalling.pytgetBiasNsc Cs6tj|jƒƒ}tj|jjƒ}g}|j|jkr‘xL|j |j|j |j dtj ƒƒD]}|j t|dƒƒqmWnxžtdt|ƒƒD]‡}||dd}||d}||krßq§nt|||ƒ}|j|jjkr§|j|jjkr§|jj |ƒq§q§WdS(sfind NFR regionstparseriiIiHN(Rtonestlengthtpysamt TabixFileR8R-R tcontigstfetchR R tasTupletappendtinttxrangetlenRRR/RR.R6( RtregionttbxtnucstrowtjRRt candidate((s;/tmp/pip-install-bGcd2k/NucleoATAC/nucleoatac/NFRCalling.pytfindNFRsTs1 *cCs9|j|ƒ|jƒ|jƒ|jƒ|jƒdS(sDwrapper to carry out all methods needed to call nucleosomes and nfrsN(R:R>RARDRW(RR8((s;/tmp/pip-install-bGcd2k/NucleoATAC/nucleoatac/NFRCalling.pytprocessds     cCs1|jjƒ}x|D]}t||ƒqWdS(s/remove data from chunk-- deletes all attributesN(t__dict__tkeystdelattr(Rtnamestname((s;/tmp/pip-install-bGcd2k/NucleoATAC/nucleoatac/NFRCalling.pyt removeDataks ( R&R'R(RR:R>RARDRWRXR^(((s;/tmp/pip-install-bGcd2k/NucleoATAC/nucleoatac/NFRCalling.pyR52s      ((R(tnumpyRRHt pyatac.tracksRRt pyatac.chunkRt pyatac.utilsRt pyatac.biasRRRRR)R5(((s;/tmp/pip-install-bGcd2k/NucleoATAC/nucleoatac/NFRCalling.pyts