def test_score_threshold(self):
# Upper bound (lower=True))
stream = fstream([(1,0.91),(2,0.45),(3,0.01)], fields=['start','score'])
res = list(score_threshold(stream,threshold=0.05,fields='score',lower=False))
expected = [(1,0.91),(2,0.45)]
self.assertListEqual(res,expected)
# Lower bound (lower=False)
stream = fstream([(1,0.91),(2,0.45),(3,0.01)], fields=['start','score'])
res = list(score_threshold(stream,threshold=0.05,fields='score',lower=True))
expected = [(3,0.01)]
self.assertListEqual(res,expected)
def __call__(self, **kw):
func = kw.get('function', "log2")
l_track = kw.get('SigMulti', {}).get('track', [])
if not isinstance(l_track, list): l_track = [l_track]
outall = []
for tname in l_track:
tinput = track(tname)
if 'score' not in tinput.fields: continue
format = kw.get('format', tinput.format)
out_name = tinput.name + '_' + func + '.' + format
outtemp = self.temporary_path(out_name)
out_track = track(outtemp, chrmeta=tinput.chrmeta)
filtered = score_threshold(tinput, strict=(func[:3] == "log"))
out_track.write(apply(filtered, 'score', eval(func)), mode='write')
out_track.close()
outall.append(outtemp)
tinput.close()
if len(outall) == 1:
self.new_file(outall[0], 'converted_track')
elif len(outall) > 1:
tar_name = self.temporary_path(fname="numeric_operation_out.tgz")
tar = tarfile.open(tar_name, "w:gz")
[tar.add(f, arcname=os.path.basename(f)) for f in outall]
tar.close()
self.new_file(tar_name, 'converted_track_tar')
return self.display_time()
def __call__(self, **kw):
func = kw.get('function',"log2")
#l_track = kw.get('SigMulti', {}).get('track',[])
l_track = kw.get('track',[])
if not isinstance(l_track, list): l_track = [l_track]
outall = []
for tname in l_track :
tinput = track(tname)
if 'score' not in tinput.fields: continue
format = kw.get('output',tinput.format)
out_name = tinput.name+'_'+func+'.'+format
outtemp = self.temporary_path(out_name)
out_track = track(outtemp,chrmeta=tinput.chrmeta)
filtered = score_threshold(tinput, strict=(func[:3] == "log"))
out_track.write(apply(filtered,'score',eval(func)), mode='write')
out_track.close()
outall.append(outtemp)
tinput.close()
if len(outall) == 1:
self.new_file(outall[0], 'converted_track')
elif len(outall) > 1:
tar_name = self.temporary_path(fname="numeric_operation_out.tgz")
tar = tarfile.open(tar_name, "w:gz")
[tar.add(f,arcname=os.path.basename(f)) for f in outall]
tar.close()
self.new_file(tar_name, 'converted_track_tar')
return self.display_time()
def test_score_threshold(self):
# Upper bound (lower=True))
stream = fstream([(1, 0.91), (2, 0.45), (3, 0.01)],
fields=['start', 'score'])
res = list(
score_threshold(stream,
threshold=0.05,
fields='score',
lower=False))
expected = [(1, 0.91), (2, 0.45)]
self.assertListEqual(res, expected)
# Lower bound (lower=False)
stream = fstream([(1, 0.91), (2, 0.45), (3, 0.01)],
fields=['start', 'score'])
res = list(
score_threshold(stream, threshold=0.05, fields='score',
lower=True))
expected = [(3, 0.01)]
self.assertListEqual(res, expected)
