# Create SVM
c = args.c[0]
kernel = args.kernel[0]
kernel_var = float(args.kernel[1])
svm = SVM(gta_profs, viral_profs, c, kernel, kernel_var)
# Print support vectors
if args.svs:
svm.show_svs()
# Xval
if args.xval:
nfolds = args.xval
if args.weight:
result = svm.xval(nfolds, NREPS, pairwiseGTA, pairwiseViral,
cluster_type, d)
else:
result = svm.xval(nfolds, NREPS)
if mini:
print("GTA Correct\tViral Correct")
print("%.2f\t%.2f" % (result[0], result[1]))
else:
print(
"We correctly classified (on average) %.2f/%d GTA and %.2f/%d Viral genes."
% (result[0], len(gta_profs), result[1], len(viral_profs)))
else: # Otherwise classify test set
# Make sure queries set
if args.queries == None:
print(
"The query file was not specified. Please declare queries using -q."
# Create SVM
c = args.c[0]
kernel = args.kernel[0]
kernel_var = float(args.kernel[1])
svm = SVM(gta_profs, viral_profs, c, kernel, kernel_var)
# Print support vectors
if args.svs:
svm.show_svs()
# Xval
if args.xval:
nfolds = args.xval
if args.weight:
result = svm.xval(nfolds, NREPS, pairwiseGTA, pairwiseViral, cluster_type, d)
else:
result = svm.xval(nfolds, NREPS)
if mini:
print("GTA Correct\tViral Correct")
print("%.2f\t%.2f" % (result[0], result[1]))
else:
print("We correctly classified (on average) %.2f/%d GTA and %.2f/%d Viral genes."
% (result[0], len(gta_profs), result[1], len(viral_profs)))
else: # Otherwise classify test set
# Make sure queries set
if args.queries == None:
print("The query file was not specified. Please declare queries using -q.")
else: # All good
# Load test set
