+[c@sdZddlZddlmZddlmZddlmZyTddlm Z ddlm Z ddlm Z dd lm Z dd lm Z WnAek rddlm Z ddlm Z ddlm Z nXd efd YZdS( s' .. module:: BuscoConfig :synopsis: Load and combine all parameters provided to BUSCO through config file, dataset and command line .. versionadded:: 3.0.0 .. versionchanged:: 3.0.1 Copyright (c) 2016-2017, Evgeny Zdobnov (ez@ezlab.org) Licensed under the MIT license. See LICENSE.md file. iN(t PipeConfig(t PipeLogger(tbusco(t NoOptionError(tNoSectionError(t ParsingError(tDuplicateSectionError(tDuplicateOptionErrort BuscoConfigc'BseZdZddddddddd d d d d ddddddddddddddddddddddd d!d"d#g'Zd$d%gZd&Zd'ZejZ d(Z id)d*6d+d,6d-d.6d/d06d1d26e j d36d4d56d6d76d6d86d6d96d6d:6d;d<6e d=6e d>6e d?6e d@6e dA6e dB6e dC6ZdDdEdFdGgZejeZedHZedIZedJZRS(KsL This class extends pipebricks.PipeConfig to read the config.ini.default file. Furthermore, it uses extra args that can be provided through command line and information available in the dataset.cfg file to produce a single instance containing all correct parameters to be injected to a busco.BuscoAnalysis instance. sçs¬s¢s´sêsîsôsŵsẑsûsâsŝsĝsĥsĵsŷsĉsésïsẅsësẗ,süsísösḧsÿsẍsèsàsäs¨s€s£sát/s'g@i Nsmailto:support@orthodb.orgitcpugMbP?tevaluetflytspeciess./tmp/ttmp_pathitlimittout_patht eukaryotatdomainsN/At clade_nametdataset_creation_datetdataset_nb_buscostdataset_nb_speciesttaugustus_parameterstlongtrestarttquiettdebugtforcettarziptblast_single_coretintoutt lineage_pathtmodec Csytt|j|Wntk rqytj||Wqtk rm}tjjd|tqXnt k r}tjjd|tnYt k r}tjjd|tn-tk r}tjjd|tnXywxz|D]r}||d&k rLt ||t k rL|jd|t||q||tkr|jd|dqqW|rxVtjD]H}y|jd|Wqtk rtjjd|tqXqWnxQ|jdD]@}|djdr|jd|dtj|dqqWd&}yatd |jdd } x| D]} | jd dd kr|jdd | jjd dqU| jd ddkry|jddWqPtk r|jdd| jjd dqPXqU| jd ddkry|jddWn7tk rm|jdd| jjd dnX| jjd d}qU| jd ddkr|jdd| jjd dqU| jd ddkr|jdd| jjd dqU| jd ddkrU|jdd| jjd dqUqUW|r|dkr|dkrtjjd|tnWnBtk r|rtjjdtjdtjdfqnXxettjjD]N}y|jd|Wqtk r8|jd|ttj|qXqWxQ|jdD]@}|djdrM|jd|dtj|dqMqMW|r>x|jD]}x|j|D]y}|djds|ddks|ddkr|dj dr3|j||dt!j"j#|dq3qqWqWn|rxN|jdD]:}|dd ksz|ddkrTtj$|dqTqTWn|rd|jddkrtjjdtqn|r1|j%dd dks|j%dd d!kr1tjjd"|j%dd tq1n|rl|j&dd#tjd#krltjjd$qlnWn;t'k rtjjd%|tntk rnXx'|jdD]}tjj(|qWd&S('s :param conf_file: a path to a config.ini.default file :type conf_file: str :param args: key and values matching BUSCO parameters to override config.ini.default values :type args: dict :param checks: whether to proceed to the mandatory parameters + file dependencies checks, used in a main BUSCO analysis. Default True :type checks: bool sError in the config file: %ss3Duplicated entry in the config.ini.default file: %sRtTruesnThe parameter '--%s' was not provided. Please add it in the config file or provide it through the command lineit_pathis %sdataset.cfgR"t=tnameRR Rt creation_dateRtnumber_of_BUSCOsRtnumber_of_speciesRt prokaryotaRsKCorrupted dataset.cfg file: domain is %s, should be eukaryota or prokaryotasThe dataset you provided does not contain the file dataset.cfg, likely because it is an old version. Default species (%s, %s) will be used as augustus speciestpathR t~R R!sPlease do not provide a full path in --out parameter, no slash. Use out_path in the config.ini.default file to specify the full path.RiszLimit must be an integer between 1 and 20 (you have used: %s). Note that this parameter is not needed by the protein mode.R s%You are using a custom e-value cutoffseNo section [busco] found in %s. Please make sure both the file and this section exist, see userguide.N()tsuperRt__init__t TypeErrorRRt_loggerterrort SystemExitRRtNonettypetbooltsettstrR$tMANDATORY_USER_PROVIDED_PARAMStgetRtitemstendswitht nice_pathtopentsplittstriptIOErrortwarningtDEFAULT_ARGS_VALUEStlisttkeystsectionst startswithtosR,t expandusertcheck_path_existtgetinttgetfloatRR( tselft conf_filetargstcheckstetkeytparamtitemRttarget_species_filetl((sJ/home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_libs/busco/BuscoConfig.pyR/>s       &   + ) - *))-       (+38  0      cCs3tjj|s/tjjd|tndS(s This function checks whether the provided path exists :param path: the path to be tested :type path: str :raises SystemExit: if the path cannot be reached sImpossible to read %sN(RHR,texistsRR1R2R3(R,((sJ/home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_libs/busco/BuscoConfig.pyRJscCs>y%|ddkr |d7}n|SWntk r9dSXdS(s :param path: a path to check :type path: str :return: the same but cleaned path :rtype str: iR N(R0R4(R,((sJ/home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_libs/busco/BuscoConfig.pyR=s   (t__name__t __module__t__doc__tFORBIDDEN_HEADER_CHARSt#FORBIDDEN_HEADER_CHARS_BEFORE_SPLITt HMMER_VERSIONt MAX_FLANKRt __version__tVERSIONtCONTACTRHtgetcwdtFalseRCR9Rt get_loggerR1R$R/t staticmethodRJR=(((sJ/home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_libs/busco/BuscoConfig.pyRs(03  &#  (RZRHt&quast_libs.busco.pipebricks.PipeConfigRt&quast_libs.busco.pipebricks.PipeLoggerRt quast_libsRt configparserRRRRRt ImportErrort ConfigParserR(((sJ/home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_libs/busco/BuscoConfig.pyt s