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"]
