ó ËdTc@s±ddlZddlZddlZddlmZddlmZddlmZm Z ddl m Z ddl m Z dfd„ƒYZ ed kr­d GHddlZndS( iÿÿÿÿN(tWig(timportr(trt FloatVector(tdeepcopy(ttimetWigscBsËeZdded„Zd„Zdded„Zddddded„Zd„Zd„Z ed „Z d dddded „Z d „Z d „Z ddd„Zd„Zd„Zddd„ZRS(icCs;i|_||_|dkr7|jd|d|ƒndS(s Parameter: file: a pathe to the directory that contain the Wiggle format files step: each chrosome will present as an vector, each value in the vector represent a short region of the chrosome, the step value is the size of the short region. tpathtsuppressN(tdatatsteptNonetload(tselfRR R((sD/oak/stanford/groups/akundaje/marinovg/programs/danpos-2.2.2/wigs.pyt__init__ s   c Cs|j}i}xR|D]J}xA||jD]2}|j|ƒrR||cd7} | G|| Gd t|| d |j| jƒƒdGHqMW|S(sÀ Description: caculate the sum of each wig's values after excluding the low and high percentile Parameter: None Value: None is=calculate total signal in each sample after excluding the tops and bottomsEpercents of genomic regions with extremely high and low signal valuesgð?itpidtbnumt nonzero_endsCcalculate total signal in each sample in genomic regions defined byt(gY@s%) ofsbase pairs calculated:s % of total)N(R RR RR RRR!taddt percentiletregionWithinValueRangetsaveRtmultiplytstrR"(R t region_filetregion_out_filetexclude_low_percenttexclude_high_percentR2R&R(R%twsumsR,twavgtrfwigtlowcutthighcuttrg((sD/oak/stanford/groups/akundaje/marinovg/programs/danpos-2.2.2/wigs.pyt samplingTotal[s: $  " $.    $? <cCs |j|S(sÁ Description: retrieve Wig class instance by name Parameter: k: the name of the Wig class instance Value: Wig class instance (R (R tk((sD/oak/stanford/groups/akundaje/marinovg/programs/danpos-2.2.2/wigs.pytget…s cCs |jjƒS(s§ Description: Retrieve the names of all Wig class instances Parameter: None Value: a list of names (R R(R ((sD/oak/stanford/groups/akundaje/marinovg/programs/danpos-2.2.2/wigs.pyRs c Cs'|}x|jdƒD] }tjj|ƒr²xîtjtjj|dƒƒD]^}tjj|ƒd}|ddkr†|d }n|j|t|d|jd|ƒƒqMWqtjj |ƒrtjj|ƒd}|ddkr÷|d }n|j|t|d|jd|ƒƒqqWdS( s Description: Load multiple Wig class instances from wiggle format files located in one directory Parameter: path: a path to the directory that contain the wiggle format files Value: None t,s*.wigiÿÿÿÿiüÿÿÿs.wigR RN( tsplittosRtisdirtglobtjointsetRR tisfile(R RRtpathstinfiletfname((sD/oak/stanford/groups/akundaje/marinovg/programs/danpos-2.2.2/wigs.pyR ™s % , tFcCs‹|dkr<t|jjƒƒdkr<|d kr<dGHdS|dkrd|jd|d|d|ƒS|dkrtd Sd t|ƒd GHd S( s" Description: normalize among Wig class instances. Parameter: nor: the normalization method, can be 'Q': quantile normalization, 'F':fold change scaling, 'S': sampling to same coverage, or 'N':no normalization Value: None tNis1less than 2 datasets, no normalization to be doneiRSR$R%R&isNormalization method s not applicable nowN(RR RR R0R:(R tnorR=R>R$R%R&((sD/oak/stanford/groups/akundaje/marinovg/programs/danpos-2.2.2/wigs.pyRU±s 3  cCs|jj|ƒS(sÇ Description: remove Wig class instance by name Parameter: k: the name of the Wig class instance that is to be removed Value: None (R R(R RF((sD/oak/stanford/groups/akundaje/marinovg/programs/danpos-2.2.2/wigs.pyRÊs c CsBtƒ}|jƒ|j}tdƒtdƒ}i}xR|D]J}xA||jD]2}|j|ƒr{||cd7s$ÿ†