def setup(self, argv):
self.set_parameters(argv[1:])
print self.set1, self.set2
print self.__dict__.items()
self.data = make_d.read_data(open(argv[0]))
self.data = make_d.assign_classes(self.data)
self.data = make_d.prepare_data(self.data)
print self.data.keys(), [len(v) for v in self.data.values()]
pass
def main(argv):
fn = argv[0]
data = make_d.prepare_data(make_d.read_data(open(fn)))
N = 10000
xdata = []
classes = []
for x in data:
xdata.extend([y for y in data[x]])
classes.extend([x for y in data[x]])
mic = compute_mic_pos_class(xdata, classes)
print mic
cmp_mic = mic
rnd_mic = [0.0 for x in mic]
for i in xrange(N):
data = make_d.prepare_data(make_d.read_data(open(fn)),
randomize='class-shuffle')
xdata = []
classes = []
for x in data:
xdata.extend([y for y in data[x]])
classes.extend([x for y in data[x]])
mic = compute_mic_pos_class(xdata, classes)
rnd_mic = map(sum, zip(rnd_mic, mic))
rnd_mic = [x/N for x in rnd_mic]
print cmp_mic
print rnd_mic
fo = open('mic.csv', 'w')
fo.write('MIC_computed,MIC_random\n')
for xy in zip(cmp_mic, rnd_mic):
print xy
fo.write('%f,%f\n' % xy)
fo.close()
return None
def main(argv):
global C_RANGE
global GAMMA_RANGE
global SET1
global SET2
i = 0
param_grid = {}
results = []
sum_acc = 0
init(argv[1:])
print SET1, SET2
# return None
fn = argv[0]
dataset = make_d.read_data(open(fn))
dataset = make_d.assign_classes(dataset)
data = make_d.prepare_data(dataset)
print data.keys(), [len(v) for v in data.values()]
param = svm.svm_parameter('-b 1')
if KERNEL_TYPE == 'LINEAR':
param.kernel_type = svm.LINEAR
GAMMA_RANGE = 1, 0, -2
else:
param.kernel_type = svm.RBF
cvfunc = leave_one_out
n_cv = None
use_sets = not SET1 is None and not SET2 is None
outfile = os.path.basename(fn)
outfile = outfile.replace('.fasta', '')
outfile = outfile.replace('.fas', '')
if use_sets:
outfile = ''.join(map(str, map(int, SET1))) + 'vs' + ''.join(map(str, map(int, SET2)))
log_name = '%s-%s-%i-%s.csv' % (TIMESTAMP,
KERNEL_TYPE,
int(RANDOMIZE_DATA),
outfile)
logfile = open(log_name, 'w')
while i < N_RUNS:
sys.stdout.write('%i ' % i)
sys.stdout.flush()
if use_sets:
""" TODO: If set sizes are reasonably large, do not use the complete smallest set. """
set1 = dict([item for item in data.items()
if item[0] in SET1])
set2 = dict([item for item in data.items()
if item[0] in SET2])
set1 = make_d.make_set(set1, training_fraction=1.0)
set2 = make_d.make_set(set2, training_fraction=1.0)
new_sets = {1.0: set1[1], -1.0: set2[1]}
sets = make_d.make_set(new_sets, training_fraction=0.75)
else:
sets = make_d.make_set(data, training_fraction=0.75)
train_y, train_x, test_y, test_x = sets
if RANDOMIZE_DATA:
random.shuffle(train_y)
random.shuffle(test_y)
pass
print [len(x) for x in sets]
def main(argv):
global C_RANGE
global GAMMA_RANGE
global SET1
global SET2
i = 0
param_grid = {}
results = []
sum_acc = 0
init(argv[1:])
print SET1, SET2
fn = argv[0]
dataset = make_d.read_data(open(fn))
dataset = make_d.assign_classes(dataset)
data = make_d.prepare_data(dataset)
print data.keys(), [len(v) for v in data.values()]
param = svm.svm_parameter('-b 1')
if KERNEL_TYPE == 'LINEAR':
param.kernel_type = svm.LINEAR
GAMMA_RANGE = 1, 0, -2
else:
param.kernel_type = svm.RBF
cvfunc = svmfun.leave_one_out
n_cv = None
limit_sets = not SET1 is None and not SET2 is None
outfile = os.path.basename(fn)
outfile = outfile.replace('.fasta', '')
outfile = outfile.replace('.fas', '')
if limit_sets:
outfile = ''.join(map(str, map(int, SET1))) + 'vs'
outfile += ''.join(map(str, map(int, SET2)))
log_name = '%s-%s-%i-%s.csv' % (TIMESTAMP,
KERNEL_TYPE,
int(RANDOMIZE_DATA),
outfile)
logfile = open(log_name, 'w')
while i < N_RUNS:
sys.stdout.write('%i ' % i)
sys.stdout.flush()
if limit_sets:
new_sets = make_d.merge_multiclasses(data, SET1, SET2)
sets = make_d.make_set(new_sets, training_fraction=0.75)
else:
sets = make_d.make_set(data, training_fraction=0.75)
train_y, train_x, test_y, test_x = sets
if RANDOMIZE_DATA:
random.shuffle(train_y)
random.shuffle(test_y)
pass
print [len(x) for x in sets]
def main(argv):
global C_RANGE
global GAMMA_RANGE
global SET1
global SET2
i = 0
param_grid = {}
results = []
sum_acc = 0
init(argv[2:])
print SET1, SET2
param = svm.svm_parameter("-b 1")
if KERNEL_TYPE == "LINEAR":
param.kernel_type = svm.LINEAR
GAMMA_RANGE = 1, 0, -2
else:
param.kernel_type = svm.RBF
cvfunc = leave_one_out
n_cv = None
use_sets = not SET1 is None and not SET2 is None
fn = argv[0]
dataset = make_d.read_data(open(fn))
data = make_d.assign_classes(dataset)
data = [(d[0], d[1][1:]) for d in data]
data = make_d.prepare_data(data)
""" Next line is just for testing. """
data = {1.0: data[1.0], 0.0: data[0.0]}
print data.keys(), [len(v) for v in data.values()]
testdata = make_d.read_data(open(argv[1]))
testset = make_d.assign_classes(testdata)
testset = [(d[0], d[1][1:]) for d in testset]
testset = make_d.prepare_data(testset)
precursor = {}
for k, v in testdata.items():
v = v[1:]
precursor[v] = precursor.get(v, []) + [int(k.split("_")[-1])]
print precursor
outfile = os.path.basename(fn)
outfile = outfile.replace(".fasta", "")
outfile = outfile.replace(".fas", "")
if use_sets:
outfile = "".join(map(str, map(int, SET1))) + "vs" + "".join(map(str, map(int, SET2)))
log_name = "%s-%s-%i-%s.csv" % (TIMESTAMP, KERNEL_TYPE, int(RANDOMIZE_DATA), outfile)
logfile = open(log_name, "w")
""" Prepare test set (precursor fragments). """
testset[-1.0] = copy.deepcopy(testset[0.0])
del testset[0.0]
testset = make_d.make_set(testset, balanced_set=False, training_fraction=1.0)
""" 'Training' and 'Test' sets flipped """
test_y, test_x = testset[:2]
encoded_x = [make_d.encode(x, make_d.encode_dic) for x in test_x]
# logfile.write(',%s\n' % ','.join(map(str, map(int, test_y))))
""" Train and predict """
row = [0.0 for x in test_x]
while i < N_RUNS:
sys.stdout.write("%i " % i)
sys.stdout.flush()
set1 = dict([item for item in data.items() if item[0] == 1.0])
set2 = dict([item for item in data.items() if item[0] == 0.0])
set1 = make_d.make_set(set1, training_fraction=1.0)
set2 = make_d.make_set(set2, training_fraction=1.0)
new_sets = {1.0: set1[1], -1.0: set2[1]}
sets = make_d.make_set(new_sets, training_fraction=1.0)
train_y, train_x, dummy_y, dummy_x = sets
print [len(x) for x in sets]
def main(argv):
global C_RANGE
global GAMMA_RANGE
init(argv[2:])
fn = argv[0]
dataset = make_d.read_data(open(fn))
items = dataset.items()
keys = [float(x[0].split('_')[0][3:]) for x in items]
dataset = zip(keys, [v[1] for v in items])
data = make_d.prepare_data(dataset)
print data.keys(), [len(v) for v in data.values()]
param = svm.svm_parameter('-b 1')
if KERNEL_TYPE == 'LINEAR':
param.kernel_type = svm.LINEAR
GAMMA_RANGE = 1, 0, -2
else:
param.kernel_type = svm.RBF
fn_test = argv[1]
testdata = make_d.read_data(open(fn_test))
testitems = testdata.items()
testkeys = [float(x[0].split('_')[0][3:]) for x in testitems]
testdataset = zip(testkeys, [v[1] for v in testitems])
testdata = make_d.prepare_data(testdataset)
cvfunc = leave_one_out
n_cv = None
outfile = os.path.basename(fn)
outfile = outfile.replace('.fasta', '')
outfile = outfile.replace('.fas', '')
log_name = '%s-%s-%i-%s.csv' % (TIMESTAMP,
KERNEL_TYPE,
int(RANDOMIZE_DATA),
outfile)
logfile = open(log_name, 'w')
i = 0
param_grid = {}
results = []
sum_acc = 0
sets = make_d.make_set(data, balanced_set=False, training_fraction=1.0)
train_y, train_x, test_y, test_x = sets
train_x = [make_d.encode(x, make_d.encode_dic) for x in train_x]
testsets = make_d.make_set(testdata, balanced_set=False,
training_fraction=0.0)
dummy0, dummy1, test_y, test_x = testsets
test_x = [make_d.encode(x, make_d.encode_dic) for x in test_x]
param_grid = {}
param_grid = grid_search(train_y, train_x, param, param_grid,
leave_one_out, n_cv, C_RANGE, GAMMA_RANGE)
ranking = []
for k, v in param_grid.items():
recognized = [v_i[0][0] == v_i[3] for v_i in v]
recog_rate = sum(map(int, recognized))/float(len(recognized))
ranking.append((recog_rate, k))
ranking.sort()
param.C, param.gamma = map(lambda x: 2**x, ranking[-1][1])
problem = svm.svm_problem(train_y, train_x)
model = svmutil.svm_train(problem, param, '-q')
result = svmutil.svm_predict(test_y, test_x, model, '-b 1')
print result
"""
cur_result = zip(result[0], test_y)
cur_acc = compute_accuracy(cur_result)
results.extend(cur_result)
total_acc = compute_accuracy(results)
sum_acc += cur_acc
mean_acc = sum_acc/(i+1)
# print cur_acc, mean_acc, total_acc
logfile.write('%f,%f,%f\n' % (cur_acc, mean_acc, total_acc))
print 'ACC', compute_accuracy(results)
"""
logfile.close()
return None
def main(argv):
do_write = True
fn = argv[0]
dataset = make_d.read_data(open(fn))
negset = make_d.read_data(open(argv[1]))
items = dataset.items()
keys = [float(x[0].split('_')[0][3]) for x in items]
dataset = zip(keys, [v[1] for v in items])
negitems = negset.items()
negkeys = [float(x[0].split('_')[0][3]) for x in negitems]
negset = zip(negkeys, [v[1] for v in negitems])
set1 = [x for x in dataset if x[0] == 1.0]
print 'Set1:', len(set1), len(set(set1))
set2 = [x for x in dataset if x[0] == 2.0]
print 'Set2:', len(set2), len(set(set2))
set4 = [x for x in dataset if x[0] == 4.0]
print 'Set4:', len(set4), len(set(set4))
set0 = [x for x in negset]
print 'Set0:', len(set0)
set1_2 = [(1.0, x[1]) for x in set1] + [(-1.0, x[1]) for x in set2]
print 'Set1_2:', len(set1_2)
if do_write: write_set(set1_2, open('1vs2.fas', 'w'))
set1_4 = [(1.0, x[1]) for x in set1] + [(-1.0, x[1]) for x in set4]
print 'Set1_4:', len(set1_4)
if do_write: write_set(set1_4, open('1vs4.fas', 'w'))
set2_4 = [(1.0, x[1]) for x in set2] + [(-1.0, x[1]) for x in set4]
print 'Set2_4:', len(set2_4)
if do_write: write_set(set2_4, open('2vs4.fas', 'w'))
set12_4 = [(1.0, x[1]) for x in set1 + set2] + [(-1.0, x[1]) for x in set4]
print 'Set12_4:', len(set12_4)
if do_write: write_set(set12_4, open('12vs4.fas', 'w'))
set14_2 = [(1.0, x[1]) for x in set1 + set4] + [(-1.0, x[1]) for x in set2]
print 'Set14_2:', len(set14_2)
if do_write: write_set(set14_2, open('14vs2.fas', 'w'))
set24_1 = [(1.0, x[1]) for x in set2 + set4] + [(-1.0, x[1]) for x in set1]
print 'Set24_1:', len(set24_1)
if do_write: write_set(set24_1, open('24vs1.fas', 'w'))
set_all = set1 + set2 + set4 + set0
print 'Set_all:', len(set_all)
if do_write: write_set(set_all, open('1vs2vs4vs0.fas', 'w'))
set124_0 = [(1.0, x[1]) for x in set1 + set2 + set4] + [(-1.0, x[1]) for x in set0]
print 'Set124_0:', len(set124_0)
if do_write: write_set(set124_0, open('124vs0.fas', 'w'))
set1_0 = [(1.0, x[1]) for x in set1] + [(-1.0, x[1]) for x in set0]
print 'Set1_0:', len(set1_0)
if do_write: write_set(set1_0, open('1vs0.fas', 'w'))
set2_0 = [(1.0, x[1]) for x in set2] + [(-1.0, x[1]) for x in set0]
print 'Set2_0:', len(set2_0)
if do_write: write_set(set2_0, open('2vs0.fas', 'w'))
set4_0 = [(1.0, x[1]) for x in set4] + [(-1.0, x[1]) for x in set0]
print 'Set4_0:', len(set4_0)
if do_write: write_set(set4_0, open('4vs0.fas', 'w'))
set12_0 = [(1.0, x[1]) for x in set1 + set2] + [(-1.0, x[1]) for x in set0]
print 'Set12_0:', len(set12_0)
if do_write: write_set(set12_0, open('12vs0.fas', 'w'))
set14_0 = [(1.0, x[1]) for x in set1 + set4] + [(-1.0, x[1]) for x in set0]
print 'Set14_0:', len(set14_0)
if do_write: write_set(set14_0, open('14vs0.fas', 'w'))
set24_0 = [(1.0, x[1]) for x in set2 + set4] + [(-1.0, x[1]) for x in set0]
print 'Set24_0:', len(set24_0)
if do_write: write_set(set24_0, open('24vs0.fas', 'w'))
return None
