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highly recommended for high-coverage isolate and multi-cell dataR s--sct single_cells0this flag is required for MDA (single-cell) datas--metaR s1this flag is required for metagenomic sample datas--bioR s1this flag is required for biosyntheticSPAdes modes--rnaR s&this flag is required for RNA-Seq datas --plasmidR s1runs plasmidSPAdes pipeline for plasmid detections --iontorrentt iontorrents)this flag is required for IonTorrent datas--testt test_modesruns SPAdes on toy datasets-hs--helpsprints this usage messages-vs --versionsprints versionR$(RRtstrRRVRRuR$(t pgroup_basicRt help_hidden((sr/oak/stanford/groups/akundaje/marinovg/programs/SPAdes-3.14.0-Linux/share/spades/spades_pipeline/options_parser.pytadd_basic_argss`           c Csd|krQ|jd|ddddd|s>d ||fntjd tnd |kr|jd |ddddd|sd ||fntjd tnd|kr|jd|ddddd|sd||fntjd tnd|krD|jd|ddddd|s1d||fntjd tnd|kr|jd|ddddd|sd||fntjd tnd|kr|jd|dd ddd|sd||fntjd tndS(!Nt12s--%s-12RBs<#>s RiRAsefile with interlaced reads for %s library number <#>. 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Will be adjusted depending on K and RL!s--read-cov-thresholdRts5read median coverage threshold (non-negative integer)s--only-generate-configtonly_generate_configs2generate configs and print script to run_spades.shs1prints this usage message with all hidden options(tsystargvRRRRRuRrRGRtcheck_dir_existenceR]RRmRt(t pgroup_hiddentshow_help_hiddent debug_grouptmismatch_correction_group((sr/oak/stanford/groups/akundaje/marinovg/programs/SPAdes-3.14.0-Linux/share/spades/spades_pipeline/options_parser.pytadd_hidden_argszs                       c Cstjdddtdddt}|jd}|jd}|jd }|jd }|jd }t|t|t|t|t ||S( NR)s spades.pytformatter_classR2s"%(prog)s [options] -o Rs Basic optionss Input datasPipeline optionssAdvanced optionssHidden options( RRR%Rtadd_argument_groupRRRRR(RORRvRRR((sr/oak/stanford/groups/akundaje/marinovg/programs/SPAdes-3.14.0-Linux/share/spades/spades_pipeline/options_parser.pyt create_parsers     cCs@tjjrtjd|ntjjr>tjd|ntjjr]tjd|ntjjr|tjd|ntjjrtjd|ntjj rtjd|ntjj rtjd|ntjj rtjd|ntjj rtjd |ntjj dk r<tjd |ndS( Ns8you cannot specify --dataset with --restart-from option!s3you cannot specify --sc with --restart-from option!s5you cannot specify --meta with --restart-from option!s8you cannot specify --plasmid with --restart-from option!s4you cannot specify --rna with --restart-from option!s8you cannot specify --isolate with --restart-from option!s;you cannot specify --iontorrent with --restart-from option!s?you cannot specify --only-assembler with --restart-from option!sFyou cannot specify --only-error-correction with --restart-from option!sVyou cannot specify strand specificity (--ss-rf or --ss-fr) with --restart-from option!(RR RRGterrorR|R R R RR}RRRR(tlog((sr/oak/stanford/groups/akundaje/marinovg/programs/SPAdes-3.14.0-Linux/share/spades/spades_pipeline/options_parser.pytcheck_options_for_restart_froms(         cCs.|jrt|nttj|jr|sdtjkrctjjdk rctj dnt j j dtj_qn1dtjkstjjdkrtj dn|st t |j}|tj|jes!Rct set_of_hmmst yaml_filenameRt correctedt gzip_outputRhR}tmax_iterationsitcount_filter_singletonsRRZt iterative_KRRlRmRtcorrect_scaffoldsRs skip-maskeds spades-bwatbwaRs output-dirtrun_truseq_postprocessing('RRRRRWR{RRRRRR RRRRtbiosyntheticspades_hmmstlistdirRRRRhR}t ITERATIONSR RRReRqRR t K_MERS_SHORTRRlRmRRRR(tcfgRtbin_homet spades_homeR t is_hmmfileR((Rsr/oak/stanford/groups/akundaje/marinovg/programs/SPAdes-3.14.0-Linux/share/spades/spades_pipeline/options_parser.pyt add_to_cfgQsp       8 '         cCstjjdr!ddl}n!tjjdrBddl}n|jr|jrtjdt j j |d|tjdt j j |d|qtjdt j j |d|tjdt j j |d |n|j rt |_n|jstjd |nt j j|jsW|jrDtjd |nt j|jn|jsf|r|jrtj|stjd |ntq)tn|jr)tjd t} | jddddd| jddtdddt| j|\} } | r)tjd|q)n|jrx|jsb|j sb|j!dkrx|j!dk rxtjd|qxn|j#r|jrtjd|qn|j|j$|j%|j#|j|j&|j'gj(t } | dkr|j|jgj(t dkrtjd|n| dkr5tj)dn|jrBdSd} t j j |jd}|rt j j*|ry|j+t,|} Wq|j-k rd} qXqn| dk r| }n|j.r\y|j+t,|j.}WnG|j-k r7tj/\}}}tjd |j.t|nXtj0|t j j1|j.}n'tj2|}tj0|t j3}||_.tj4||j5p|j#|j6|tj7|t8j9stjd!n|j#r-t:|t:tj7|t8j;kr-tjd"d#j t8j;d$q-n|jr|j< rt:tj7|d%dkst:|t=dt:tj7|d&d'd(gdkrtjd)qn| dkrt,|j.d*/}|j>||d+td,d-d.t?d/WdQXnt@|S(0Ns2.is3.s-1stest_dataset_plasmid/pl1.fq.gzs-2stest_dataset_plasmid/pl2.fq.gzstest_dataset/ecoli_1K_1.fq.gzstest_dataset/ecoli_1K_2.fq.gzsGthe output_dir is not set! 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