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)
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, \
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)
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:
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)