ó €vIc@sadZddlZddlZddlZddlmZddlmZddd„ƒYZdS(s. This module allows you to control Simcoal2. i’’’’N(tcopyfile(tdebugtSimCoalControllercBs eZd„Zddd„ZRS(cCsŠ||_tj|_tj|jƒ}|jdksEtjdkrpd|_g|D]}|jƒ^qU}n d|_|j|krĄtj |jtj |jtj ƒsĢt dƒ‚qĢn t dƒ‚dS(s¹Initializes the controller. simcoal_dir is the directory where simcoal is. The initializer checks for existance and executability of binaries. tnttcygwins simcoal2.exetsimcoal2sSimCoal not executablesSimCoal not availableN( t simcoal_dirtostnametos_nametlistdirtsystplatformtbin_nametlowertaccesstseptX_OKtIOError(tselfRt dir_contentstx((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PopGen/SimCoal/Controller.pyt__init__s   " t1t.cCsæ|dkr-tjjtjddgƒ}ntjƒ}tj|ƒ|jtj|j d|dt |ƒd|}t j dkr—|d7}n |d7}tj |ƒtj|ƒdS(sExecutes SimCoal. tSimCoaltrunst twin32s > nul 2>nuls >/dev/null 2>&1N(tNoneRRtjointConfigtdataDirtgetcwdtchdirRR tstrR R tsystem(Rtpar_filetnum_simstployditpar_dirtcurr_dirtcmd((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PopGen/SimCoal/Controller.pyt run_simcoal+s !  5   (t__name__t __module__RR+(((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PopGen/SimCoal/Controller.pyRs (( t__doc__RR ttempfiletshutilRtloggingRR(((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PopGen/SimCoal/Controller.pyt s