Example #1
0
    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, \
                         mapreads.MapReads, \
                         findorfs.FindORFS, findreps.FindRepeats, annotate.Annotate, \
                         abundance.Abundance, fannotate.FunctionalAnnotation, scaffold.Scaffold, \
                         findscforfs.FindScaffoldORFS, propagate.Propagate, \
                         classify.Classify, postprocess.Postprocess], verbose=1)

       if not utils.getFromPath("dot", "Graphviz") == "":
          pipeline_printout_graph (   'flowchart.svg',
                               'svg',
Example #2
0
    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)

    try:

       dlist = []
       #pipeline_printout(sys.stdout,[preprocess.Preprocess],verbose=1)                                                                                                                           
       tasks_to_run = ["preprocess.Preprocess"]

       if "ASSEMBLE" in skipsteps or "Assemble" in skipsteps or "assemble" in skipsteps or "asm" in skipsteps:
           pass
       else:
           tasks_to_run.append("assemble.Assemble")
Example #3
0
                  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)
    postprocess.init(readlibs, skipsteps, selected_programs["classify"])
    generic.init(skipsteps, readlibs)

    try:

        dlist = []
        #pipeline_printout(sys.stdout,[preprocess.Preprocess],verbose=1)
        tasks_to_run = ["preprocess.Preprocess"]

        if "ASSEMBLE" in skipsteps or "Assemble" in skipsteps or "assemble" in skipsteps or "asm" in skipsteps:
            pass
        else:
            tasks_to_run.append("assemble.Assemble")