def init(): model_setting = { "model_def": "/data/share/lenet_40000/deploy.prototxt", "pretrained_model": "/data/share/lenet_40000/lenet_iter_40000.caffemodel", "images_dim": "48,48", "raw_scale": "255.0", "input_scale": "0.00390625", "label_file": "/data/share/lenet_40000/synset.txt", } classify.CLASSIFIER, classify.LABEL_FILE = classify.init(model_setting)
def init(): model_setting = { "model_def": "/data/share/lenet_40000/deploy.prototxt", "pretrained_model": "/data/share/lenet_40000/lenet_iter_40000.caffemodel", "images_dim": "48,48", "raw_scale": "255.0", "input_scale": "0.00390625", "label_file": "/data/share/lenet_40000/synset.txt" } classify.CLASSIFIER, classify.LABEL_FILE = classify.init(model_setting)
def detect(): gc.collect() imgBytes = request.data imgdata = base64.b64decode(imgBytes) with open("temp.png", 'wb') as f: f.write(imgdata) f.close() print("successfully receieved image") # Pass image bytes to classifier result = classify.analyse("temp.png") # Return results as neat JSON object, using result = jsonify(result) print(result.json) response_data = result.json return response_data if __name__ == '__main__': init() try: port = os.environ['PORT'] except: port = "8080" app.run(host='0.0.0.0', port=port, debug=False)
# 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:
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', [postprocess.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: 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:
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) postprocess.init(readlibs, skipsteps, selected_programs["classify"]) generic.init(skipsteps, readlibs) try:
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) 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"]