ó ?îec@stdZddlmZmZddlZddlmZddljZ de fd„ƒYZ dd d„ƒYZ dS( sG VMat Class @author: Alicia Schep, Greenleaf Lab, Stanford University iÿÿÿÿ(tsignaltndimageN(tcopyt VMat_ErrorcBs eZdZd„Zd„ZRS(s!Class for errors in VMat functioncCs ||_dS(N(tvalue(tselfR((s1/tmp/pip-install-bGcd2k/NucleoATAC/pyatac/VMat.pyt__init__scCs t|jƒS(N(treprR(R((s1/tmp/pip-install-bGcd2k/NucleoATAC/pyatac/VMat.pyt__str__s(t__name__t __module__t__doc__RR(((s1/tmp/pip-install-bGcd2k/NucleoATAC/pyatac/VMat.pyRs tVMatcBs­eZdZd„Zd„Zd„Zdd„Zdd„Zddd„Zd „Z d „Z d „Z dddd „Z dd „Zdd„Zd„Zed„ƒZRS(s.Class for storing and processing V-plot matrixcCsY|jd||kr&tdƒ‚n||_||_||_|jdd|_dS(sà Assumes Vplot is centered! Inputs: mat = matrix (as numpy array) lower = lower bound of insert sizes represented by mat upper = upper bound of insert sizes represented by mat is.mat shape is not consistent with insert limitsiiN(tshapeRtmattuppertlowertw(RRRR((s1/tmp/pip-install-bGcd2k/NucleoATAC/pyatac/VMat.pyRs    cCsÌ||j}||j}|j|}|j|d}||jjdks||dks||dks|||jjdkr‹tdƒ‚n|j||…||…f|_||_||_||_dS(s—reduce the size of the vplot lower is new lower bound upper is new upper bound w is new flanking region around center iis Mat is smaller than desired trimN(RRRR RR(RRRRtuptdntlefttright((s1/tmp/pip-install-bGcd2k/NucleoATAC/pyatac/VMat.pyttrim&s   D"  cCsTxMt|j|jƒD]6}||j}|ddkrÀ|j|d|jd…f|j||jd…fddd…d}tj||d ddd…fƒ|j|dd…f icCs%tjj|j|ddƒ|_dS(s#smooth v-plot using gaussian kernelR$tconstantN(Rtfilterstgaussian_filterR(Rtsd((s1/tmp/pip-install-bGcd2k/NucleoATAC/pyatac/VMat.pytsmoothZscCs(tjj|j||ddƒ|_dS(s!smooth v-plot along one axis onlyR$tnearestN(RR(tgaussian_filter1dR(RR*taxis((s1/tmp/pip-install-bGcd2k/NucleoATAC/pyatac/VMat.pytsmooth1d^scCs’|jtj|jƒ}tj|jjƒd|jj}|jtj|j|ƒtj|j|ƒ|_|j|jjdd|_dS(sanormalize v matrix so that signal minus even background will be 1 divided by base pairs in windowgð?ig$@N(RRtsumtonesR tsize(Rttmp1ttmp2((s1/tmp/pip-install-bGcd2k/NucleoATAC/pyatac/VMat.pytnormbs#4cCsdx]t|jjdƒD]E}|j||jd||jƒtj|j|ƒ|j|VMat decriptor file appeas to be missing someneeded components( RatinttstriptappendRdtfloatRYR Rtarrayt NameErrorRRK(RMtinfiletstateRtlineRRR%((s1/tmp/pip-install-bGcd2k/NucleoATAC/pyatac/VMat.pyRa¿s2            /   N(R R R RRRR&R+R/R5R8R=RBROR]R`Rgt staticmethodRa(((s1/tmp/pip-install-bGcd2k/NucleoATAC/pyatac/VMat.pyR s          (( R tscipyRRtnumpyRRtmatplotlib.pyplottpyplotRCR#RR (((s1/tmp/pip-install-bGcd2k/NucleoATAC/pyatac/VMat.pyts