Esempio n. 1
0
    import validate
    import multialign
    import findorfs
    import findreps
    import abundance
    import annotate
    import fannotate
    import scaffold
    import findscforfs
    import propagate
    import classify
    import postprocess

    # initialize submodules
    preprocess.init(readlibs, asmcontigs, skipsteps, selected_programs["assemble"], run_fastqc,selected_programs["preprocess"])
    assemble.init(readlibs, skipsteps, selected_programs["assemble"], asmcontigs, userKmerSupplied == False)
    mapreads.init(readlibs, skipsteps, selected_programs["mapreads"], savebtidx,ctgbpcov,lowmem)
    validate.init(readlibs, skipsteps, selected_programs["validate"], asmScores)
    findorfs.init(readlibs, skipsteps, selected_programs["findorfs"], min_ctg_len, min_ctg_cvg,read_orfs)
    findreps.init(readlibs, skipsteps)
    multialign.init(readlibs, skipsteps, forcesteps, selected_programs["multialign"],refgenomes)
    annotate.init(readlibs, skipsteps, selected_programs["annotate"], nofcpblast)
    fannotate.init(skipsteps)
    abundance.init(readlibs, skipsteps, forcesteps, selected_programs["annotate"])
    scaffold.init(readlibs, skipsteps, retainBank)
    findscforfs.init(readlibs, skipsteps, selected_programs["findorfs"])
    propagate.init(readlibs, skipsteps, selected_programs["annotate"])
    classify.init(readlibs, skipsteps, selected_programs["annotate"], lowmem, 0 if not isolate_genome else 100)
    postprocess.init(readlibs, skipsteps, selected_programs["annotate"])
    generic.init(skipsteps, readlibs)
Esempio n. 2
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    import assemble
    import mapreads
    import findorfs
    import findreps
    import abundance
    import annotate
    import fannotate
    import scaffold
    import findscforfs
    import propagate
    import classify
    import postprocess

    # initialize submodules
    preprocess.init(readlibs, skipsteps, selected_programs["assemble"], run_fastqc,filter)
    assemble.init(readlibs, skipsteps, selected_programs["assemble"], usecontigs)
    mapreads.init(readlibs, skipsteps, selected_programs["assemble"], selected_programs["mapreads"], savebtidx,ctgbpcov,lowmem)
    findorfs.init(readlibs, skipsteps, selected_programs["assemble"], selected_programs["findorfs"], min_ctg_len, min_ctg_cvg)
    findreps.init(readlibs, skipsteps)
    annotate.init(readlibs, skipsteps, selected_programs["classify"], nofcpblast)
    fannotate.init(skipsteps)
    abundance.init(readlibs, skipsteps, forcesteps, selected_programs["classify"])
    scaffold.init(readlibs, skipsteps, retainBank, selected_programs["assemble"])
    findscforfs.init(readlibs, skipsteps, selected_programs["findorfs"])
    propagate.init(readlibs, skipsteps, selected_programs["classify"])
    classify.init(readlibs, skipsteps, selected_programs["classify"])
    postprocess.init(readlibs, skipsteps, selected_programs["classify"])

    try:
       dlist = []
       pipeline_printout(sys.stdout,[preprocess.Preprocess,assemble.Assemble, \
Esempio n. 3
0
    import findreps
    import abundance
    import classify
    import classifyreads
    import fannotate
    import scaffold
    import findscforfs
    import propagate
    import bin
    import postprocess

    # initialize submodules
    preprocess.init(readlibs, asmcontigs, skipsteps,
                    selected_programs["assemble"], run_fastqc,
                    selected_programs["preprocess"])
    assemble.init(readlibs, skipsteps, selected_programs["assemble"],
                  asmcontigs, (userKmerSupplied == False and isolate_genome))
    mapreads.init(readlibs, skipsteps, selected_programs["mapreads"],
                  savebtidx, ctgbpcov, lowmem)
    benchmark.init(readlibs, skipsteps, availableRulers_dict["classifyreads"])
    validate.init(readlibs, skipsteps, selected_programs["validate"],
                  asmScores)
    findorfs.init(readlibs, skipsteps, selected_programs["findorfs"],
                  min_ctg_len, min_ctg_cvg, read_orfs)
    findreps.init(readlibs, skipsteps)
    multialign.init(readlibs, skipsteps, forcesteps,
                    selected_programs["multialign"], refgenomes)
    classify.init(readlibs, skipsteps, selected_programs["classify"],
                  nofcpblast)
    classifyreads.init(readlibs, skipsteps, selected_programs["classifyreads"],
                       nofcpblast)
    fannotate.init(skipsteps)
Esempio n. 4
0
    import findorfs
    import findreps
    import abundance
    import annotate
    import fannotate
    import scaffold
    import findscforfs
    import propagate
    import classify
    import postprocess

    import shutil

    # initialize submodules
    preprocess.init(readlibs, skipsteps, selected_programs["assemble"], run_fastqc,filter)
    assemble.init(readlibs, skipsteps, selected_programs["assemble"], usecontigs)
    mapreads.init(readlibs, skipsteps, selected_programs["assemble"], selected_programs["mapreads"], savebtidx,ctgbpcov,lowmem)
    findorfs.init(readlibs, skipsteps, selected_programs["assemble"], selected_programs["findorfs"], min_ctg_len, min_ctg_cvg,read_orfs)
    findreps.init(readlibs, skipsteps)
    multialign.init(readlibs, skipsteps, forcesteps, selected_programs["multialign"],refgenomes)
    annotate.init(readlibs, skipsteps, selected_programs["annotate"], nofcpblast)
    fannotate.init(skipsteps)
    abundance.init(readlibs, skipsteps, forcesteps, selected_programs["annotate"])
    scaffold.init(readlibs, skipsteps, retainBank, selected_programs["assemble"])
    findscforfs.init(readlibs, skipsteps, selected_programs["findorfs"])
    propagate.init(readlibs, skipsteps, selected_programs["annotate"])
    classify.init(readlibs, skipsteps, selected_programs["annotate"], lowmem)
    postprocess.init(readlibs, skipsteps, selected_programs["annotate"])
    generic.init(skipsteps, readlibs)

    try:
Esempio n. 5
0
    import abundance
    import classify
    import classifyreads
    import fannotate
    import scaffold
    import findscforfs
    import propagate
    import bin
    import postprocess

    # initialize submodules
    preprocess.init(
        readlibs, asmcontigs, skipsteps, selected_programs["assemble"], run_fastqc, selected_programs["preprocess"]
    )
    assemble.init(
        readlibs, skipsteps, selected_programs["assemble"], asmcontigs, (userKmerSupplied == False and isolate_genome)
    )
    mapreads.init(readlibs, skipsteps, selected_programs["mapreads"], savebtidx, ctgbpcov, lowmem)
    benchmark.init(readlibs, skipsteps, availableRulers_dict["classifyreads"])
    validate.init(readlibs, skipsteps, selected_programs["validate"], asmScores)
    findorfs.init(readlibs, skipsteps, selected_programs["findorfs"], min_ctg_len, min_ctg_cvg, read_orfs)
    findreps.init(readlibs, skipsteps)
    multialign.init(readlibs, skipsteps, forcesteps, selected_programs["multialign"], refgenomes)
    classify.init(readlibs, skipsteps, selected_programs["classify"], nofcpblast)
    classifyreads.init(readlibs, skipsteps, selected_programs["classifyreads"], nofcpblast)
    fannotate.init(skipsteps)
    abundance.init(readlibs, skipsteps, forcesteps, selected_programs["classify"])
    scaffold.init(readlibs, skipsteps, retainBank)
    findscforfs.init(readlibs, skipsteps, selected_programs["findorfs"])
    propagate.init(readlibs, skipsteps, selected_programs["classify"])
    bin.init(readlibs, skipsteps, selected_programs["classify"], lowmem, 0 if not isolate_genome else 100)