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)