ó ¥Á^c@seddlZddlZddlZddlZdefd„ƒYZd„Zd„Zd„ZdS(iÿÿÿÿNtCommandcBs>eZdddd„Zd„Zd„Zd„Zd„ZRS(tcCsy||_||_||_||_||_||_|jdkrQg|_n||_|jdkrug|_ndS(N(tSTAGEtpathtargst short_namet config_dirt del_aftertNonet output_files(tselfRRRRRRR ((ss/oak/stanford/groups/akundaje/marinovg/programs/SPAdes-3.14.0-Linux/share/spades/spades_pipeline/commands_parser.pyt__init__s        cCs|jg|jS(N(RR(R ((ss/oak/stanford/groups/akundaje/marinovg/programs/SPAdes-3.14.0-Linux/share/spades/spades_pipeline/commands_parser.pytto_listscCsdj|jƒƒS(Nt (tjoinR (R ((ss/oak/stanford/groups/akundaje/marinovg/programs/SPAdes-3.14.0-Linux/share/spades/spades_pipeline/commands_parser.pyt__str__"scCstj|jƒ|ƒdS(N(tsupporttsys_callR (R tlog((ss/oak/stanford/groups/akundaje/marinovg/programs/SPAdes-3.14.0-Linux/share/spades/spades_pipeline/commands_parser.pytrun%scCsJi|jd6|jd6|jd6|jd6|jd6|jd6|jd6S(NRRRRRR R(RRRRRR R(R ((ss/oak/stanford/groups/akundaje/marinovg/programs/SPAdes-3.14.0-Linux/share/spades/spades_pipeline/commands_parser.pytto_dict(s      N(t__name__t __module__RR R RRR(((ss/oak/stanford/groups/akundaje/marinovg/programs/SPAdes-3.14.0-Linux/share/spades/spades_pipeline/commands_parser.pyRs    cCsQt|dƒ<}|jdƒx%|D]}|j|jƒdƒq&WWdQXdS(Ntwsset -e s (topentwriteR(tcommandst output_filetfwtcommand((ss/oak/stanford/groups/akundaje/marinovg/programs/SPAdes-3.14.0-Linux/share/spades/spades_pipeline/commands_parser.pytwrite_commands_to_sh2s  c Cs“tjjdƒr!ddl}n!tjjdƒrBddl}ng|D]}|jƒ^qI}t|dƒ}|j||dtƒWdQXdS(Ns2.iÿÿÿÿs3.Rtdefault_flow_style( tsystversiont startswithtpyyaml2tpyyaml3RRtdumptFalse(RRtyamlRtdatatf((ss/oak/stanford/groups/akundaje/marinovg/programs/SPAdes-3.14.0-Linux/share/spades/spades_pipeline/commands_parser.pytwrite_commands_to_yaml9scCs”tjjdƒr!ddl}n!tjjdƒrBddl}nt|ƒ}|j|ƒ}WdQXg}x!|D]}|jt|ƒqsW|S(Ns2.iÿÿÿÿs3.( R R!R"R#R$RtloadtappendR(t yaml_fpathR'tstreamR(Rtkwargs((ss/oak/stanford/groups/akundaje/marinovg/programs/SPAdes-3.14.0-Linux/share/spades/spades_pipeline/commands_parser.pytread_commands_from_yamlEs ( trandomtstringRR tobjectRRR*R0(((ss/oak/stanford/groups/akundaje/marinovg/programs/SPAdes-3.14.0-Linux/share/spades/spades_pipeline/commands_parser.pyt s    "