a hQ@sddlZddlZddlZddlmZddlmZddlmZmZddlZddl Z ddl m Z ddZ dd Z d d ZGd d d ejZddZGdddejZGdddejZGdddejZddZddZddZddZddZd d!Zd"d#Zd$d%Zd&d'Zd(d)ZdQd+d,Z d-d.Z!d/d0Z"d1d2Z#d3d4Z$d5d6Z%d7d8Z&d9d:Z'd;d<Z(d=d>Z)dRd?d@Z*dSdAdBZ+dTdCdDZ,dEdFZ-dGdHZ.dIdJZ/dKdLZ0dMdNZ1dOdPZ2dS)UN)gettext)basename)abspath expanduser) empty_configcCsxd}ttjd}tj}tjdd}|jdddd|jdd dd|jd d dd|jd d dd|jdddd|jdddd|jdddd|jdddd|jdddd||\}}|dks|jrd }nL|dks|jrd}n8|dks|j rd }n$|j r d}n|dks|j r"d }|dksD|j r<|j sD|j rHd}|dksZ|j r^d}|dksp|jrtd}|S) NrFadd_help --isolateisolate store_truedestaction--rnarna --plasmidplasmid--metameta--biobio --metaviral metaviral --metaplasmid metaplasmid --rnaviralrnaviral--coronacoronaz rnaspades.pyzrnaviralspades.pyzplasmidspades.pybgcz metaspades.pyzmetaplasmidspades.pyzmetaviralspades.pyzcoronaspades.py)roptions_storagefirst_command_lineargparseArgumentParser add_argumentparse_known_argsrrrrrrrr)modeZscript_basenameoptionsZ mode_parsernargs unknown_argsr*m/home/psgendb/BIRCHDEV/install/SPAdes-4.2.0-Linux/linux-x86_64/share/spades/spades_pipeline/options_parser.pyget_modes> "r,cCst}|dkrd|_n|dkr&d|_n|dkrz0ConcatenationAction.__call__..r]rautoz2cann't set 'auto' and kmers' size at the same time)rcr"rqrbr rrr*r*r+rls   zConcatenationAction.__call__)NNNNNFNN)Nrmr*r*r<r+rssrscCsf|dkr|gSt|}|tjks*|tjkrBtd|tjtjf|ddkr\td||gSdS)Nrxz:wrong k value %d: all k values should be between %d and %dr3rz,wrong k value %d: all k values should be odd)intr MIN_KMAX_Kr"ArgumentTypeError)rjkr*r*r+kmers  r~cCsP|}|ddkr|dd}|d}tt|D]}t||d||<q2|S)Nr[,r)rdrangercr~)rjk_mersir*r*r+kmerss   rcCs|dkr |St|SdS)Nrx)ryrjr*r*r+qvoffsetsrcCsD|dks|dkr|St|r2t|dkr2t|Std|dS)NrxoffzGwrong value %s (should be a positive float number, or 'auto', or 'off')r^is_floatfloatr"r|rr*r*r+ cov_cutoffs rcCs0t|rt|dkrt|Std|dS)Nrz2wrong value %s (should be a positive float number)rrr*r*r+ lcer_cutoffsrcCs6|tjvr2|tjkr2|ds2td|tjf|S)Nr}z>wrong value %s (should be 'ec', 'as', 'k', 'mc', or '%s'))r SHORT_STAGES_NAME LAST_STAGE startswithr"r|rr*r*r+ restart_fromsrcCs&|tjvr"|ds"td||S)Nr}z8wrong value %s (should be 'ec', 'as', 'k', or 'mc'))r rrr"r|rr*r*r+ stop_aftersrcCs0t|rt|dkrt|Std|dS)Nrz8wrong value %s (should be a non-negative integer number))r^is_intryr"r|rr*r*r+read_cov_thresholdsrc Cs tddD]}dD]^}|jd||fddtjtd|jd||fddtjtd|jd||fddtjtdqd D]X}|jd||fd tjtd |jd||fd tjtd |jd||fd tjtd qv|jd |ddtjtd|jd |ddtjtdq dS)Nr] )z-12-1-2rVz--pe%d%s rUr(rTrz--mp%d%sz --hqmp%d%s)z-frz-rfz-ffr)r(rTrz--s%dz--pe%d-m)rr$r"SUPPRESSrL)pgroup_input_datanumZsufix orientationr*r*r+add_deprecated_input_data_argss`  rc Cst}|jdddtddtd|du}|jdd|s6dntjd d |jd d |sRd ntjd d |jdd|sndntjd d |jdd|sdntjd d |jdd|sdntjd d |jdd|sdntjd d |jdd|sdntjd d |jdd|sdntjd d |jd d!|sd"ntjd d |jd#d$|s6d%ntjd d |jd&d'|sTd(ntjd d |jd)d*d+d d |jd,d-d.d d |jd/d0d1d2d3|jd4d5d6d7td8dS)9N-oz z5directory to store all the resulting files (required) output_dir)rUrTrQrPr rr r zMthis flag is highly recommended for high-coverage isolate and multi-cell datar r rTrz--sc single_cellz0this flag is required for MDA (single-cell) datarrz*this flag is required for metagenomic datarrz1this flag is required for biosyntheticSPAdes modez--sewagesewagez%this flag is required for sewage moderrz+this flag is required for coronaSPAdes moderrz&this flag is required for RNA-Seq datarrz1runs plasmidSPAdes pipeline for plasmid detectionrrz1runs metaviralSPAdes pipeline for virus detectionrrzoruns metaplasmidSPAdes pipeline for plasmid detection in metagenomic datasets (equivalent for --meta --plasmid)rrz9this flag enables virus assembly module from RNA-Seq dataz --iontorrent iontorrentz)this flag is required for IonTorrent dataz--test test_modezruns SPAdes on toy datasetz-hz--helpzprints this usage messagerTrTrz-vz --versionzprints versionr1)rTrr1)r,r$strrnr"rr1) pgroup_basicr& help_hiddenr*r*r+add_basic_args srFcCs4d|vr2|jd|dd|s&d||fntjtdd|vrd|jd|dd|sXd ||fntjtdd |vr|jd |dd|sd ||fntjtdd |vr|jd|dd|sd||fntjtdd|vr|jd|dd|sd||fntjtdd|vr0|jd|dd|s$d||fntjtddS)N12z--%s-12<#>rr3zefile with interlaced reads for %s library number <#>. Older deprecated syntax is -%s<#>-12 r1z--%s-1zafile with forward reads for %s library number <#>. Older deprecated syntax is -%s<#>-1 2z--%s-2zafile with reverse reads for %s library number <#>. Older deprecated syntax is -%s<#>-2 sz--%s-szbfile with unpaired reads for %s library number <#>. Older deprecated syntax is -%s<#>-s mz--%s-mz`file with merged reads for %s library number <#>. Older deprecated syntax is -%s<#>-m r\z--%s-or)rzzkorientation of reads for %s library number <#> ( = fr, rf, ff). Older deprecated syntax is -%s<#>-)r$r"rrL)Zlibidnamesuffixesrrr*r*r+add_library_argsts       rcCs$t}|jddddtd|jddddtd|jdddd td|jd ddd td|jd ddd tdt||dv}tddgd||jddddtdtddgd||tddgd|||jddd|sdntjtd|dk}|jddddtd|jd ddd!td|d"k}|jd#dd|s2d$ntjtd|jd%dd|sRd&ntjtd|dk}|jd'dd|szd(ntjtd|jd)d*d+d,d-g|sd.ntjd/d0|jd1d*d+d,tjd2d3|jd4d+d-tjd2d5|d6ko|d7ko|d8ko|d9k}|jd:dd|sd;ntjtddS). Older deprecated syntax is --s<#> mpz mate-pair)rrrrr\hqmpzhigh-quality mate-pairz--sangerzfile with Sanger readsrz--pacbiozfile with PacBio readsz --nanoporezfile with Nanopore readsrz--trusted-contigszfile with trusted contigsz--untrusted-contigszfile with untrusted contigsz--fl-rnazFfile with PacBio/Nanopore/contigs that capture full-length transcriptsz--sszstrand_specificityfrrfzestrand specific data, = fr (normal) and rf (antisense). Older deprecated syntax is --ss-store)rUr rRrTrz--ss-frZ store_const)rUr rOrTrz--ss-rf)r rOrTrrrrrz--assembly-graphzfile with assembly graph)r,r$rLrrr"r)rr&rr*r*r+add_input_data_argss &rc CsXt}|dkp|dk}|jddd|s(dntjdd|jdd d|sFd ntjdd|d v}|}|jd d d|stdntjdd|jdd dtjdd|jdddddd|jddddddtj}|dvrdtj}|jddd dt|dd!|}|jd"d#dd$dd|jd%d#dtjdd|}|jd&d'dd(dd|jd)d'dtjdddS)*Nrrz--only-error-correctiononly_error_correctionz4runs only read error correction (without assembling)r r rPrTrz--only-assembleronly_assemblerz4runs only assembling (without read error correction)rrrz --carefulcarefulz5tries to reduce number of mismatches and short indelsz--careful:false store_falsez --checkpointsz checkpointsz.save intermediate check-points ('last', 'all')rrUr rTr --continue continue_modezNcontinue run from the last available check-point (only -o should be specified)rzfrestart run with updated options and from the specified check-point ('ec', 'as', 'k', 'mc', '%s'))rrzZrestart run with updated options and from the specified check-point ('as', 'k', '%s')--restart-fromr)rUr rPrQrTrz--disable-gzip-outputdisable_gzip_outputz;forces error correction not to compress the corrected readsz--disable-gzip-output:falsez --disable-rr disable_rrz.disables repeat resolution stage of assemblingz--disable-rr:false)r,r$r"radd_mutually_exclusive_groupr rr)pgroup_pipeliner&rZ careful_groupZrestart_from_helpZdisable_gzip_output_grouprr*r*r+add_pipeline_argssrc Cst}|jddtjdddd|jddd d td tjdd |jd dd tddtjdd|jdddddd|jdd ddtdtj dt d|dv}|jddt dd|sd nt j dd!|jd"d#d$td%dd |jd&dd'd(dd)|}|jd*d+dd,d-d.|jd/d+dt j d0d.dS)1Nz --datasetrdataset_yaml_filenamez,file with dataset description in YAML formatrrUrQr rTrz-tz --threadsthreadsz!number of threads. [default: %s] rUr rQrTrz-mz--memorymemoryzCRAM limit for SPAdes in Gb (terminates if exceeded). [default: %s] z --tmp-dirz z:directory for temporary files. [default: /tmp]tmp_dir)rUrTr rz-kr+zDlist of k-mer sizes (must be odd and less than %d) [default: 'auto']r])rUr r(rQrTrrz --cov-cutoffrzUcoverage cutoff value (a positive float number, or 'auto', or 'off') [default: 'off'])rUrQrPr rTrz--phred-offsetz <33 or 64>rzJPHRED quality offset in the input reads (33 or 64), [default: auto-detect]z --custom-hmms custom_hmmszEdirectory with custom hmms that replace default ones, [default: None]rz--gfa11gfa11z&use GFA v1.1 format for assembly graphr rz --gfa11:falser)r,r$r^check_file_existenceryr THREADSMEMORYrr{rsrr"rrr)pgroup_advancedr&rrr*r*r+add_advanced_argsfs  rcCs*dtjv}|}|jddd|r$dntjdd|jdddtjdd|jd d d|rXd ntjdd|jd d dt|rxdntjdd|}|jddd|rdntjdd|jdddtjdd|jdddtj|rdntjdd|jdddtj|rdntjdd|jdddtj |rd ntjdd|jd!d"d#t |r>d$ntjdd|jd%d&d'|r^d(ntjdd|jd)d*d|r~d+ntjdd|jd,d-t d.|rd/ntjdd0|jd1d"d2t |rd3ntjdd|jd4d5|rd6ntjdd7|jd8d9|rd:ntjdd7|jd|rd;ntjdN --help-hiddenz--debugdeveloper_modezruns SPAdes in debug moder rz --debug:falserz --trace-time time_tracerzenable time trackerz --stop-afterrrzRruns SPAdes until the specified check-point ('ec', 'as', 'k', 'mc') inclusiverrz--mismatch-correctionmismatch_correctorz>runs post processing correction of mismatches and short indelsz--mismatch-correction:falsez --referencer referencez:file with reference for deep analysis (only in debug mode)z--series-analysisseries_analysisz3config for metagenomics-series-augmented reassemblyz --configs-dirz Z configs_dirzdirectory with configsz--read-buffer-sizerread_buffer_sizez/sets size of read buffer for graph constructionz--large-genome large_genomeFz'Enables optimizations for large genomesz --save-gpsave_gpzIEnables saving graph pack before repeat resolution (even without --debug)z--hidden-cov-cutoffrrzcoverage cutoff value deeply integrated in simplification (a positive float number). Base coverage! Will be adjusted depending on K and RL!rz--read-cov-thresholdrz5read median coverage threshold (non-negative integer)z--only-generate-configonly_generate_configz2generate configs and print script to run_spades.shrz--no-clear-afterno_clear_afterz5don't delete tmp files after SPAdes pipeline finishedz1prints this usage message with all hidden optionsrTr) sysargvrr$r"rrr^rcheck_dir_existenceryrr) pgroup_hiddenshow_help_hiddenZ debug_groupZmismatch_correction_groupr*r*r+add_hidden_argss rc Cs|jddddddd|jdd d d d dd|jd ddtdddd|jddddd|jddddd dd|jdddd d ddd!tjv}|jd"d#d|rd$ntjd%|jd&d'd|rd(ntjd%|jd)d*d|rd+ntjd%dS),Nz --grid-enginez grid_enginelocalzOrun under grid control ('slurm', 'local', 'mpi', save_yaml') [default: 'local']r)rUr rPrTrz --grid-queuezZ grid_queueZstandardz/submits the jobs to one of the specified queuesz --grid-nnodesrZ grid_nnodesr3z"specifies the number of processors)rUr rQrPrTrz --grid-wait grid_waitzwait for job finishr rz --grid-extraZ grid_extrarXzany extra commands)r rPrTrUrz --grid-timeZ grid_timez1:00:00z time limitrz--grid-profileZ grid_profilezFenable mpi task profiling (for SLURM grid engine, for developers only))r rrTz--grid-valgrindZ grid_valgrindzGrun mpi tasks with valgrind (for SLURM grid engine, for developers onlyz--grid-coredumpZ grid_coredumpzGenable core dumps for mpi tasks (for SLURM cluster, for developers only)r$ryrrr"r)pgroup_clusterrr*r*r+add_cluster_args"sr    rcCstjdtddd}|d}|d}|d}|d}|d }|d }t|t|t|t|t|t ||S) Nz spades.pyz"%(prog)s [options] -o F)r:Zformatter_classrCrz Basic optionsz Input datazPipeline optionszAdvanced optionszCluster execution optionszHidden options) r"r#r2Zadd_argument_grouprrrrrr)rfrrrrrrr*r*r+ create_parserYs       rcCsdtjvr"tjjdur"td|tjjr6td|tjjrJtd|tjjr^td|tjjrrtd|tjj rtd|tjj rtd|tjj rtd |tjj rtd |tjj rtd |tjjdurtd |dS) NrWz[you cannot specify input data (-1, -2, -12, --pe-1, --pe-2 ...) with --restart-from option!z8you cannot specify --dataset with --restart-from option!z3you cannot specify --sc with --restart-from option!z5you cannot specify --meta with --restart-from option!z8you cannot specify --plasmid with --restart-from option!z4you cannot specify --rna with --restart-from option!z8you cannot specify --isolate with --restart-from option!z;you cannot specify --iontorrent with --restart-from option!z?you cannot specify --only-assembler with --restart-from option!zFyou cannot specify --only-error-correction with --restart-from option!zVyou cannot specify strand specificity (--ss-rf or --ss-fr) with --restart-from option!)r r-rWr^errorrrrrrr rrrr)logr*r*r+check_options_for_restart_fromos,           rcCs|jrt|ttj|jrT|stdtjvrBtjjdurBtdt j dtj_n dtjvsjtjjdurttd|st t |j}|tj |j<t|d||_|jdurt t |j}|tj |j<t|d||_|jdurt t |j}t|d||_d|vr"|jdur"d |_|jr0d |_|jrJ|jrJtd |jsZ|jrn|jrntd ||jr|jrtd ||jd kr|jd krtd|jd kr|jd krtd|jr|js|jrtd||jr|js |jrtd||jr0|jr0td|jrJ|jrJtd|jdur\d |_|jdurp|j|_|js|js|jr|jsd |_dS)Nrz/you cannot specify -o and --test simultaneouslyZ spades_testGthe output_dir is not set! It is a mandatory parameter (-o output_dir).zoutput directoryzdirectory for temporary fileszdirectory with custom hmmsrTzNyou cannot specify --only-error-correction and --only-assembler simultaneouslyz;you cannot specify --only-error-correction in RNA-seq mode!z;you cannot specify --only-error-correction in isolate mode!FzKyou cannot specify --mismatch-correction and --careful:false simultaneouslyzKyou cannot specify --mismatch-correction:false and --careful simultaneouslyzFyou cannot specify --mismatch-correction or --careful in RNA-seq mode!zFyou cannot specify --mismatch-correction or --careful in isolate mode!zLIsolate mode already implies --only-assembler, so this option has no effect.zHRNA mode already implies --only-assembler, so this option has no effect.)rrr.r r-rrr^rospathrrdict_of_rel2abscheck_path_is_asciirrrrrrrrrr rrwarningrr)r-rskip_output_dirrrrr*r*r+ add_to_optionsh                      rcst|d<t|d<|js$t|d<|js4t|d<|j|djd<|j|djd<|j|djd<|j|djd<|j|djd <|j |djd <|j |djd <t j |d |djd <|j|djd<|jr|j|djd<d|jdur|jn2|jrt j |tjn|jr*t j |tjdurd}ddt j rpd fddt D}nr~}|dkrtd|||djd<|j|djd<|j r|jr|j|djd<|jsxt j |djd|djd<|j |djd<|jr"|j|djd<|j|djd<tj|djd<|j sR|j!r`d|djd <|j"rx|j"|djd!<|jsP|j#d"kr|j$durd|_#|j#r|j#|djd#<n0|j%s|j&rd"|djd#<ntj'|djd#<|j(|djd$<|j)|djd%<|j*|djd&<|j+|djd'<|j"r@|j"|djd!<|j,|djd(<|js|j-rt|d)<d|d)jd*<t j |d+|d)jd,<|j|d)jd-<|j|d)jd.<dS)/Ncommondataseterror_correctionassemblyrrr max_threads max_memoryrrzsewage/usher_barcodes.csvZ sewage_matrixrrrXcSs\tj|oZ|dpZ|dpZ|dpZ|dpZ|dpZ|dpZ|dpZ|dS) NZhmmzhmm.gzZaazaa.gzZfazfa.gzZfnazfna.gz)rrisfileendswith)hmmfiler*r*r+s zadd_to_cfg..rcs,g|]$}tj|rtj|qSr*)rrjoin)rtrZ hmms_pathZ is_hmmfiler*r+rvszadd_to_cfg..zXCustom HMM folder does not contain any HMMs. They should have .hmm or .hmm.gz extension.Z set_of_hmms yaml_filenamerZ corrected gzip_outputrrmax_iterationsr]Zcount_filter_singletonsrrx iterative_Krrrrrrz skip-maskedz spades-bwaZbwarz output-dir).rrrrrprrrrrrrrr rrrrr biosyntheticspades_hmmsrcoronaspades_hmmsisdirlistdirr^rrrrrr ITERATIONSrrrrrrr K_MERS_SHORTrrrrrr)cfgrbin_home spades_homer-Zhmmsr*r r+ add_to_cfgs           rc Cs~ddl}|jrv|jrFtdtj|d|tdtj|d|n0tdtj|d|tdtj|d||js|j rd|_ |j st d |tj |j s|jrt d |t|j |js|r|jrt|st d |tntnZ|jrVtjd d } | jdddd| jdtdtd| |\} } | rVt d| ||j r|js|js|jdkr|jdurt d||js|j r|jrt d||j|j|j|j |j|j |j |j!|j"|j#|j|j$g %d} | dko|j |j|j#g%ddk} | dko2|j |jg%ddk}| dkoV|j |j|j"g%ddk}| dkov|j |j g%ddk}| dko|j |j |j!g%ddk}| dko|j |j |j!|j$g%ddk}| dks| s|s|s|s|s|st d|n| dkrt&d|jr dSd}tj|j d}|rvtj'|rvz|(t)|}Wn|j*ytd}Yn0|t+_,|j-rz|(t)|j-t+_,Wn<|j*yt./\}}}t d |j-t|Yn0t0t+j,tj1|j-t+_,n"t2t+j,t+_,t0t+j,t3t+_,|dur&|}nt+j,}||_-t4||j5pD|j|j6|t7|t+j8sht d!|jrt9|t9t7|t+j:krt d"d#t+j:d$|j r$|j;s$|j s$td,d-Wdn1sj0Yt?|S).Nrrztest_dataset_plasmid/pl1.fq.gzrztest_dataset_plasmid/pl2.fq.gzztest_dataset/ecoli_1K_1.fq.gzztest_dataset/ecoli_1K_2.fq.gzTrzBthe output_dir should exist for --continue and for --restart-from!z4you cannot specify reads with --restart-from option!Frrrr r rrrQr rzyou cannot specify any option except -o with --continue option! Please use '--restart-from last' if you need to change some of the options from the initial run and continue from the last available checkpoint. Extra options: %srzXyou cannot specify --careful, --mismatch-correction or --cov-cutoff in metagenomic mode!z-you cannot specify --careful in RNA-Seq mode!rZr3r]zWSpecified mode combination is not supported! Check out user manual for available modes.zxNo assembly mode was specified! If you intend to assemble high-coverage multi-cell/isolate data, use '--isolate' option.zinput_dataset.yamlz/exception caught while parsing YAML file (%s): zYyou should specify at least one unpaired, paired-end, or high-quality mate-pairs library!z)you cannot specify any data types except , z in RNA-Seq mode!rzassembly-graphpacbionanoporezyou cannot specify any data types except a single paired-end library (optionally accompanied by a single library of PacBio reads or Nanopore reads) in metaSPAdes mode!w"inf)default_flow_style default_styler;)@pyyaml3rrr^rerrr rrrrrrrmakedirsrdataset_is_emptysave_restart_optionsload_restart_optionsr"r#r$rrnr%rrrrrrr rrrrcountrrloadopen YAMLErrorr original_dataset_datarrexc_inforelative2abs_pathsdirnamecorrect_datasetgetcwdcheck_dataset_readsrrget_lib_ids_by_type READS_TYPES_USED_IN_CONSTRUCTIONrcREADS_TYPES_USED_IN_RNA_SEQrmaxdumprset_default_values)r-rrWrrload_processed_datasetrr'pyyamlcontinue_parserr(r)Z modes_countZis_metaplasmidZis_bgcZ is_metaviralZ is_rnaviralZ is_coronaZ is_sewageZexisting_dataset_dataZprocessed_dataset_fpath_excZpaired_end_libsZ graph_libsZlong_read_libsfr*r*r+postprocessing.s        ( $ $ $(.            &r@c Cst}t}|r tjj}tjj} |} |} ||\t_} tjjdurz|sztjjD]} |j fi| diqP||\t_} | rd}| |d | |r|tj_| tj_t tj|| dtjvrtjj }nt}ttj||||| ||}tjjrtjddfSt||||tjtj||fS)NzIPlease specify option (e.g. -1, -2, -s, etc)) for the following paths: %srrW)rJrr r-rrr%rrpZ set_defaultsrr rrWrKr@rr)rrrsecondary_fillingrr'rrfZold_output_dirZold_stop_afterrr:rrjmsgrWr*r*r+ parse_argss:    rCcCst}|dSr6)rZ print_help)r/Z show_hiddenr&rfr*r*r+rCsrCcCstjjdurtjtj_tjjdurNtrDtttj ttj_n tj tj_tjj durbdtj_ tjj durvdtj_ tjj durdtj_ tjj durdtj_ tjjdurdtj_tjjdurdtj_tjjdurdtj_tjjdkrdtj_tjjdurdtj_tjjdur*tjtjjtjtj_tjjdur@dtj_tjjdurVdtj_tjjdurldtj_tjjdurdtj_dS)NFZnonerxr)r r-rrrr^get_available_memoryryminrrrrrrrrrrrrrr rTMP_DIRrrrrr*r*r*r+r9sD            r9cCs4tjfittjt_dtj_dtj_dtj_dSr6) r"Z Namespacevarsr r-restartrrrr*r*r*r+r'sr'cCs|dtjvrFtjjrFtjjt_tjjdkr2dtj_n tjjtj_dtj_tjjD](}tjj|durNtjj|tjj|<qNdS)Nrrx)r rHrr-original_k_mersrp)optionr*r*r+r(s     r(cCs*|D] \}}|dks|drdSqdS)NrrTF)r)r'rkrjr*r*r+ will_reruns   rKcCsNtjdd}|jdddd|jdddtd d |\}}|jpJ|jdu S) NFrrrr r rrr)r rPrQr)r"r#r$rr%r)r<r(r)r*r*r+ is_first_runs   rLcCsFtjdd}|jdtdtd|\}}|jdur8dStt|jS)NFrrrr) r"r#r$rrnr%rrr)Z output_parserr(r)r*r*r+get_output_dir_from_args#s    rM)F)N)FN)FN)3rrr"rZos.pathrrrr^r Z process_cfgrr,r.r1rAr2rKZActionrLrnrsr~rrrrrrrrrrrrrrrrrrrr@rCrCr9r'r(rKrLrMr*r*r*r+ sZ   $ &    -T 6pLKq7I^ { * &