ó ËdTc @sddlZddlZddlZddlZddlmZddlmZddlmZdedd„Z d„Z dedd„Z d dd d eeded ed „ Z d d„Zd d„Zedkrüejejjƒddƒe_ndS(iÿÿÿÿN(tWig(tglob(ttimei c Cs¿tƒ}|dkrŸdG|GdGH|d d}td|d|d|d |ƒ} | jd|ƒ| jd|d d d|d |ƒd Gtƒ|GHtƒ}n|}d G|GdGH|d d} x tjj| ƒrâ| d} qÃWtj| ƒ|dkr-d|dt |ƒdt | ƒd|} n d|dt | ƒd|} tj | ƒ|dkr‡dG|GdGHtj d|ƒndG| GHtj dt | ƒdƒd Gtƒ|GHdS(Ntwigs convertings...iýÿÿÿsraw.wiqtfiletgfiletsteptsuppresstformattwiqs time cost:s sortingttemps.tempssort -r -n -s -k1 -k2 -o s --buffer-size s --temporary-directory t s Removing srm tremovings -r( RRt ajust_sizetsavetostpathtisdirtmkdirtNonetstrtsystem( tifilet sort_ofileRRRRtbufferttmt raw_ofiletwgR tcmd((sC/oak/stanford/groups/akundaje/marinovg/programs/danpos-2.2.2/wiq.pytrawsorts2   !"    1     c Cs dGHtƒ}|jdƒ}i}t|dƒ}x|D]}t|ƒ|||d d ksŸ|d d ksŸ|d dkr¬|d}qoWtjj ||ƒ}|dksÚ|tkr0|d d ||d d [optional arguments] for more help, please try: python danpos wig2wiq -h itformatter_classtusagesH python danpos.py [optional arguments] t descriptionttepilogsÍKaifu Chen, et al. chenkaifu@gmail.com, Li lab, Biostatistics department, Dan L. Duncan cancer center, Baylor College of Medicine.tcommandtdefaultthelps8set as 'wig2wiq' to convert wiggle format to wiq format.tchr_filesJa text file with each line describing a chrosome length, e.g. 'chr1 10043't input_pathssÌpaths to the wiggle format input files. Each path could point to a file or a directory that contains the files. use ':' to seperate paths, e.g. 'Path_A:path_Bs --out_dirtdestRJtmetavartwig2wiqsa path to the output directorys--stepRi ttypes$the step size in wiggle format data.s --buffer_sizeRsUmaximal memory size that can be used to sort file, e.g. set to 1 when need 1G memory.s is5 for more help, please try: python danpos wig2wiq -h s0 for help, please try: python danpos wig2wiq -h s command: pythonR R'RRRON(R"tsystargvtargparsetArgumentParsertArgumentDefaultsHelpFormattert add_argumentRR4R#t print_helpt parse_argsRERXRbRaRJRRCRRB(R^tparsertargs((sC/oak/stanford/groups/akundaje/marinovg/programs/danpos-2.2.2/wiq.pyRersP3 $$     cCsåttjƒdkr<dtjkr<dtjkr<dGHdStjdtjddd d d d ƒ}|jd dd<ddƒ|jddd<ddƒ|jddd<ddƒ|jddddd ddddƒ|jddddd dd<ddƒ|jddddd dd dd!ƒ|jd"dd#dd dd dd$ƒ|jd%dd&dd ddd'tdd(ƒ|jd)dd*dd ddd'tdd+ƒ|jd,dd-dd dd.d'tdd/ƒ|jd0dd1dd dd.d't dd2ƒdtjks dtjkr$d3GH|j ƒd3GHdSttjƒd4kr\y|j ƒ}Wqed5GHdSXn d6GHdSd7Gd8j tjƒGHt d9|jd:|jd|jd|jd|jd#|jd&|jd*|jd-|jd;td1|jƒ d<S(=sÍ Description: This function parses input parameters, calls and passes all parameters values to the function qnorwig, or print some help messages if required. parameters: none is-hs--helpsz usage: python danpos.py wiq [optional arguments] for more help, please try: python danpos wiq -h iRYRZsI python danpos.py [optional arguments] R[R\R]sÍKaifu Chen, et al. chenkaifu@gmail.com, Li lab, Biostatistics department, Dan L. Duncan cancer center, Baylor College of Medicine.R^R_R`sAset as 'wiq' to do quantile normalization for wiggle format data.RasJa text file with each line describing a chrosome length, e.g. 'chr1 10043'Rbsîpaths to the input files, each file shoule be in '.wig' or '.wiq' format. Each path could point to a file or a directory that contains the files. use ':' to seperate paths, e.g. 'Path_A:path_Bs --out_dirRcRJRdR>sa path to the output directorys --referenceR6s¿a path to the file containing reference data. When reference data is available, data in each input file will be normalized to have the same quantiles in reference datas --iformatRKRs5the data format in input files, can be 'wig' or 'wiq's --rformatRLs8the data format in reference file, can be 'wig' or 'wiq's --isortedRMRfs4set to 1 if the input file in wiq format and sorted.s --rsortedRNs;set to 1 if the reference file is in wiq format and sorted.s--stepRi s$the step size in wiggle format data.s --buffer_sizeRsUmaximal memory size that can be used to sort file, e.g. set to 1 when need 1G memory.s is1 for more help, please try: python danpos wiq -h s, for help, please try: python danpos wiq -h s command: pythonR R'RRN(R"RgRhRiRjRkRlRR4R#RmRnRERXRbRaRJR6RKRLRMRNRRCR(R^RoRp((sC/oak/stanford/groups/akundaje/marinovg/programs/danpos-2.2.2/wiq.pyR ¹sl3 $$$$         t__main__Ri(RRgRFRiRRRRRCRRR1R=RXReR t__name__tfdopentstdouttfileno(((sC/oak/stanford/groups/akundaje/marinovg/programs/danpos-2.2.2/wiq.pyts0 '- G R