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mcat_test.py
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mcat_test.py
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#! /usr/bin/python
# batch tester for synthetic data
# by: jake martinez (jrm98)
from seq_gen import generate
from statfile import StatFile
import subprocess, os, time, sys
import matplotlib as mpl
mpl.use('Agg')
import matplotlib.pyplot as plt
def accuracy(found,motifs):
if found in motifs:
return 1.0
# for m in motifs:
# possible options:
# - 2/3/4-mer counts
# - 1-(edit distance/motif length)
return 0.0
def test(name,w=12,N=15,n=500,e=0,ep=.65,P=1,minloc=0,maxloc=-1,
directory='test/data/',negative=False,nmotifs=1,dyad=False,threshold=2, log=None):
seqfilename = 'testdata_'+name+'.fasta'
negfilename = 'testdata_'+name+'_neg.fasta'
if log is not None:
log.write('[%s]: Using sequences file "%s"\n' % (time.strftime('%H:%M:%S'),seqfilename) )
log.flush()
#generate sequences file
(sequences,motifs) = generate(w,N,n,e=e,ep=ep,P=P,minloc=minloc,
maxloc=maxloc, output=seqfilename,
directory=directory,negative=negative,nmotifs=nmotifs,dyad=dyad)
#generate complementary negative sequences file
(nsequences,_) = generate(w,N,n,output=negfilename,
directory=directory,negative=True)
#run pipeline for test data
cmdLine = "python orange_pipeline.py "+directory+seqfilename+" "+directory+negfilename+" -s test/stat > test/logs/output.log 2> test/logs/output_error.log"
if log is not None:
log.write('[%s]: Beginning command "%s"\n' % (time.strftime('%H:%M:%S'),cmdLine) )
log.flush()
subprocess.call([cmdLine], shell=True)
if log is not None:
log.write('[%s]: Looking through statdir\n' % time.strftime('%H:%M:%S'))
log.flush()
statdir='test/stat' # path to stat directory
statfiles = sorted([ f for f in os.listdir(statdir) if f.startswith('stat_')])
if len(statfiles) <= 0:
return None
sf_filename = str(statfiles[0])
sf_id = sf_filename.replace('stat','').replace('.','').replace('_','')
if log is not None:
log.write('[%s]: Found StatFile "%s"\n' % (time.strftime('%H:%M:%S'),sf_filename) )
log.flush()
sf = StatFile('test/stat/'+sf_filename)
return sf
# judge how well motif was found based on top three results
# for i in range(1,4):
# found = sf.get_by('rank',i)
# acc = accuracy(found['motif'],motifs)
# if acc > 0.50:
# return acc / (2**(i-1)) # adjust accuracy score based on rank
# return 0.0
def graph_res(res,name):
points = []
for (x,sf) in res:
sf.load()
ys = sf.sort_by('pval')[:20] # get 20 rows with best pvals
for y in ys:
points.append( (x,y) )
fig = plt.figure(figsize=(7,7))
ax = fig.add_subplot(111)
ax.scatter(points)
ax.set_xlabel(name)
ax.set_ylabel('p-Value')
fig.savefig('test/img/%s.png'%name)
def test_width(motifprob, guessed_width, interval=2,
start=6, stop=20, numtests=10, log=None):
res = []
for width in range(start, stop, interval):
for x in range(numtests):
res.append( (width,test('width'+str(width)+'-'+str(x),w=width,P=motifprob, log=log)) )
graph_res(res,'width')
return res
def test_mprob(guessed_width, interval=1, granularity=0.1,
start=0.1, count=10, numtests=10, log=None):
res = []
vals = [start+(x*granularity) for x in range(count)]
for motifprob in vals:
for x in range(numtests):
res.append( (motifprob,test('mprob'+str(motifprob)+'-'++str(x),w=guessed_width,P=motifprob, log=log)) )
graph_res(res,'mprob')
return res
def test_eprob(max_e, guessed_width, interval=1, granularity=0.1,
start=0.1, count=10, numtests=10, log=None):
res = []
vals = [start+(x*granularity) for x in range(count)]
for eprob in vals:
for x in range(numtests):
res.append( (eprob,test('eprob'+str(eprob)+'-'++str(x),w=guessed_width,e=max_e,ep=eprob, log=log)) )
graph_res(res,'eprob')
return res
def test_mloc(mloc, guessed_width, motifprob=.9, interval=2,
start=6, stop=20, numtests=10, log=None):
res = []
for mloc in range(start, stop, interval):
for x in range(numtests):
res.append( (mloc,test('mloc'+str(mloc)+'-'++str(x),w=guessed_width,P=motifprob, log=log)) )
graph_res(res,'mloc')
return res
def test_nmotifs():
pass
def parse_results():
try:
with open('results/results.html','r') as f:
lines = f.readlines()
results = []
for line in lines:
if 'Motif:' in line:
m = line.replace('Motif:','').replace(' ','').replace('\n','')
results += [m]
return results
except Exception:
print 'file not found...'
return results
def editdist(string1,string2):
pass
def cleanup():
subprocess.call(["./test/cleanup_syn_batch.sh"], shell=True)
pass
def main():
print 'mcat_test: beginning synthetic batch test...'
#test results
res = []
#parameters for synthetic data
testname = ''
numtests = 10
w = 8
N = 100
n = 500
e = 5
eprob = .55
P = 1
nmotifs = 1
dyadmode = False
directory = 'test/data'
#check for batch test data directory, create if doesn't exist
if not os.path.exists(os.path.join(os.getcwd(),directory)):
sys.stdout.write('mcat_test: creating test data directory...\n')
os.makedirs(directory)
if not os.path.exists(os.path.join(os.getcwd(),'test/img')):
sys.stdout.write('mcat_test: creating test img directory...\n')
os.makedirs('test/img')
if not os.path.exists(os.path.join(os.getcwd(),'test/logs')):
sys.stdout.write('mcat_test: creating test logs directory...\n')
os.makedirs('test/logs')
if not os.path.exists(os.path.join(os.getcwd(),'test/stat')):
sys.stdout.write('mcat_test: creating test logs directory...\n')
os.makedirs('test/stat')
with open('test/logs/test.log','w') as log:
#motif width sensitivity
sys.stdout.write('mcat_test: running motif width sensitivity tests...')
sys.stdout.flush()
begin = time.time()
res += test_width(.9, 12, log=log)
end = time.time()
sys.stdout.write('Done (%fs).\n' % (end-begin))
sys.stdout.flush()
#motif probability sensitivity
sys.stdout.write('mcat_test: running motif probability sensitivity tests...')
sys.stdout.flush()
begin = time.time()
res += test_mprob(12, log=log)
end = time.time()
sys.stdout.write('Done (%fs).\n' % (end-begin))
sys.stdout.flush()
#motif error sensitivity
sys.stdout.write('mcat_test: running motif error sensitivity tests...')
sys.stdout.flush()
begin = time.time()
res += test_eprob(5, 12, log=log)
end = time.time()
sys.stdout.write('Done (%fs).\n' % (end-begin))
sys.stdout.flush()
#motif location sensitivity
# sys.stdout.write('mcat_test: running motif location sensitivity tests...')
# sys.stdout.flush()
# begin = time.time()
# res += test_mloc(12)
# end = time.time()
# sys.stdout.write('Done (%fs).\n' % (end-begin))
# sys.stdout.flush()
pass
if __name__ == '__main__':
try:
main()
except Exception as err:
with open('log.txt','w') as f:
f.write(str(err))