spec = 0.0
print "%5.4f" % spec,
print "PPV:",
try:
ppv = float(self.getProp('num.Feature.Hits.TP')) / self.getProp(
'num.Feature.Hits')
except ZeroDivisionError:
ppv = 0.0
print "%5.4f" % ppv
# -----------------------------------------------------------------------
# main()
# Generate Motif object from patterns
motiflist = map(lambda x: Motif.Motif(x), patternlist)
globalAnalysis = SummaryAnalysis('TOTAL')
globalAnalysis.displayHeadings()
# Load Sitefile
siteFile = SiteFile(sitefilename)
# Open PDB dbh
pdbdbh = proteindatabankdbh.dbopen()
# For each PDB
for pdbid in pdblist:
print >> sys.stderr, pdbid
if motiflist:
# TRAIN SVM
print("TRAIN SVM")
Cobj = SVM(xtrain, y_train)
Cobj.train(C=1.)
Cobj.svm_save("results/svm_trained.pkl")
# COMPUTE gPOIM
print("COMPUTE gPOIM")
small_k = 2
Pobj = gPOIM()
Pobj.set_up(Cobj, samplesize=100, small_k=small_k)
Pobj.save("results/gPOIM.pkl")
# PLOT gPOIM
view.plot_gPOIM(Pobj.gPOIM, "results/gPOIM.pdf")
# EXTRACT Motif
print("EXTRACT MOTIF")
motif_start, motif_len = get_motif_pos_len_similar_diffPOIM(Pobj.gPOIM)
motif_len = [20]
Mobj = Motif()
motif = Mobj.find(2,
motif_len,
Pobj.gPOIM,
motif_start,
base=['A', 'C', 'G', 'T'])
np.savetxt("results/pwm.pkl", motif[0])
seqLogo("results/pwm.pkl")