Examples by Tasks¶
All implemented modes are associated with examples, check “pyEnGNet examples” for more information.
Run on CPU¶
“tests/test_integration/test_cpu.py” demonstrates the basic API for the generation of co-expression gene networks using CPUs.
Load gene co-expression dataset from input file
from pyengnet.File import File dataset = File.load(path=os.getcwd()+"/datasets/Spellman.csv", separator=",", nmi_th=0.6, spearman_th=0.7, kendall_th=0.7, readded_th=0.7, hub_th = 3)
Run pyEnGNet based on CPUs.
from pyengnet.Engnet import Engnet graphFiltered, infoGraphFiltered, graphComplete, infoGraphComplete = Engnet.process(dataset, saveComplete = True)
Save gene co-expression networks output (optional)
from pyengnet.File import File File.saveFile(path='/home/user/Desktop/graphComplete.csv',graph=infoGraphComplete) File.saveFile(path='/home/user/Desktop/graphFiltered.csv',graph=infoGraphFiltered)
Print gene co-expression networks output (optional)
from pyengnet.File import File File.showGraph(graph=graphComplete,title='Complete graph') File.showGraph(graph=graphFiltered,title="Filtered graph")
Run on GPU devices¶
“tests/test_integration/test_gpu.py” demonstrates the basic API for the generation of co-expression gene networks using GPU devices.
Load gene co-expression dataset from input file
from pyengnet.File import File dataset = File.load(path=os.getcwd()+"/datasets/Spellman.csv", separator=",", nmi_th=0.6, spearman_th=0.7, kendall_th=0.7, readded_th=0.7, hub_th = 3)
Run pyEnGNet based on CPUs.
from pyengnet.Engnet import Engnet graphFiltered, infoGraphFiltered, graphComplete, infoGraphComplete = Engnet.process(dataset, saveComplete = True, numGpus = 2, computeCapability = 61)
Save gene co-expression networks output (optional)
from pyengnet.File import File File.saveFile(path='/home/user/Desktop/graphComplete.csv',graph=infoGraphComplete) File.saveFile(path='/home/user/Desktop/graphFiltered.csv',graph=infoGraphFiltered)
Print gene co-expression networks output (optional)
from pyengnet.File import File File.showGraph(graph=graphComplete,title='Complete graph') File.showGraph(graph=graphFiltered,title="Filtered graph")