import sys
import os
from ContactUtils import TopAccuracy
from ContactUtils import LoadContactMatrix
if __name__ == "__main__":
if len(sys.argv) < 3:
print 'python EvaluateContactAccuracyTXT.py predContactMatrixFile_txt nativeContactMatrixFile_txt [targetName]'
print ' This script evaluates the accuracy of a predicted contact matrix by comparing it with native contact matrix'
print ' Both matrix files are in text format with L lines and each line has L columns where L is the protein sequence length'
exit(1)
predFile = sys.argv[1]
nativeFile = sys.argv[2]
if len(sys.argv) > 3:
target = sys.argv[3]
else:
target = os.path.basename(nativeFile).split('.')[0]
pred = LoadContactMatrix(predFile)
truth = LoadContactMatrix(nativeFile)
accs = TopAccuracy(pred, truth)
accsStr = [str(a) for a in accs]
resultStr = target + ' ' + str(pred.shape[0]) + ' TopAcc '
resultStr += (' '.join(accsStr))
print resultStr
def str_display(ls):
if not isinstance(ls, (list, tuple, np.ndarray)):
str_ls = '{0:.4f}'.format(ls)
return str_ls
str_ls = ['{0:.4f}'.format(v) for v in ls ]
str_ls2 = ' '.join(str_ls)
return str_ls2
if __name__ == "__main__":
if len(sys.argv) != 4:
print 'python CalcMCCF1.py pred_matrix_file distcb_matrix_file target'
print ' Both matrix files are text format with L lines and each line has L columns where L is the protein sequence length'
exit(-1)
predFile = sys.argv[1]
distcbFile = sys.argv[2]
target = sys.argv[3]
pred = LoadContactMatrix(predFile)
truth = LoadContactMatrix(distcbFile)
for prob in np.arange(20, 60, 2):
#print "prob=", prob
accs = CalcMCCF1(pred=pred, truth=truth, probCutoff=prob/100.)
resultStr = target + ' ' + str(pred.shape[0]) + ' cutoff=' + str(prob) + ' ' + str_display(accs)
print resultStr
print '\t\twhen the suffix is .txt or .ccmpred, it is a text matrix file with L rows and L columns where L is protein length and each entry shall be predicted confidence/probability of being a contact'
print '\t\twhen the suffix is .predictedDistMatrix.pkl, it is a file in cPickle format containing a tuple of at least 6 items: name, sequence, predictedDistProbMatrix, predictedContactProbMatrix, labelWeight and labelDistribution'
print '\tgroundTruthFile: the ground truth file in text or cPickle format, usually ending with .native.pkl'
print'\t\twhen it is a text format, its content shall be distance matrix instead of contact matrix, i.e., a large value indicates a non-contact and -1 indicates an invalid entry'
exit(1)
predFile = sys.argv[1]
nativeFile = sys.argv[2]
if len(sys.argv)>3:
target = sys.argv[3]
else:
target = os.path.basename(nativeFile).split('.')[0]
if predFile.endswith('.txt') or predFile.endswith('.ccmpred'):
predCbCbContactMatrix = LoadContactMatrix(predFile)
elif predFile.endswith('.pkl'):
with open(predFile, 'rb') as fh:
pred = cPickle.load(fh)
predCbCbContactMatrix = pred[3]['CbCb']
else:
print 'ERROR: predFile shall end with .txt or .pkl'
exit(1)
if nativeFile.endswith('.txt'):
nativeCbCbDistMatrix = LoadContactMatrix(nativeFile)
elif nativeFile.endswith('.pkl'):
with open(nativeFile, 'rb') as fh:
truth = cPickle.load(fh)
nativeCbCbDistMatrix = truth['atomDistMatrix']['CbCb']
else: