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',
[postprocess.Postprocess],
no_key_legend = True)
# 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")
if "FINDORFS" in skipsteps or "FindORFS" in skipsteps or "findorfs" in skipsteps:
pass
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")
if "FINDORFS" in skipsteps or "FindORFS" in skipsteps or "findorfs" in skipsteps:
pass