def test_run(self):
"""sliding, no matching"""
a = gelscore.Sequence('GYPMGGYPMGGYPMGGYPMGGYPMG')
b = gelscore.Sequence('AAAAA')
fac = slide.SequenceCompositionComparatorFactory()
scb = fac.make(b, 'sequence')
sw = slide.SequenceWindow(a, 5)
res = sw.slide(scb)
self.assertAlmostEqual(sum(res.scores), 0.0)
def test_run(self):
"""iterating"""
a = gelscore.Sequence('ACDEFGHIKLAAAAAAAAAAAMNPQRSTVWY')
#b = gelscore.Sequence('AAAAA')
winsize = 5
sw = slide.SequenceWindow(a, winsize)
xi = 0
while sw.isValid():
seq = sw.currentSequence()
#print seq, str(a[xi:(xi+winsize)])
self.assertTrue(str(seq) == str(a[xi:(xi + winsize)]))
sw.next()
xi += 1
def test_run(self):
"""sliding, no matching"""
a = gelscore.Sequence(
'QLAQQIQARNQMRYQQATAAAAAAAAGMPGQFMPPMFYGVMPPRGVPFNGPNPQQMNPMGGMPKNGMPPQFRNGPVYGVPPQGGFPRNANDNNQFYQ'
)
b = gelscore.Sequence('MPQNGRA')
fac = slide.SequenceCompositionComparatorFactory()
scb = fac.make(b, 'sequence')
sw = slide.SequenceWindow(a, len(b))
ress = sw.slide(scb)
for (xi, res) in enumerate(ress.results()):
self.assertTrue(a[res.position - 1] == a[xi])
self.assertTrue(res.score >= 0.0)
dout.addHeader('orf', 'S. cerevisiae systematic name', 's')
dout.addHeader('n.above', 'Number of windows with score >= threshold', 'd')
dout.addHeader(
'max.score',
'Maximum score (1 - chi-squared histogram distance on normalized aa-composition histograms)',
'f')
dout.addHeader(
'max.position',
'1-based sequence position of window (start of window) having the maximum score',
'd')
dout.describeHeader(data_outs)
dout.writeHeader(data_outs)
for orf in query_keys:
seq = gelscore.Sequence(prot_dict[orf])
sw = slide.SequenceWindow(seq, options.window_size)
# Slide window and collect results
slideres = sw.slide(comparator)
# Anything interesting?
n_above = 0
max_score = 0.0
max_pos = None
for res in slideres.results():
if res.score > max_score:
max_score = res.score
max_pos = res.position
if res.score >= options.score_threshold:
n_above += 1
# Write out results
# Find stretches of sequence that are above threshold in score
line = "{:s}\t{:d}\t{:1.4f}\t{:d}\n".format(orf, n_above, max_score,
def test_run(self):
"""searching"""
a = gelscore.Sequence('ACDEFGHIKLAAAAAAAAAAAMNPQRSTVWY')
sw = slide.SequenceWindow(a, 5)
res = sw.search()
self.assertTrue(str(res.currentSequence()) == 'AAAAA')
def test_run(self):
"""window larger than sequence"""
a = gelscore.Sequence(
'MLSLIFYLRFPSYIRG') # Actual protein sequence YJR151W-A
sw = slide.SequenceWindow(a, 20)
for k in query_keys:
prot_dict[k] = prot_dict[k].replace("-",'')
if options.debugging:
query_keys = query_keys[0:min(len(query_keys,100))]
# Set up motif to compare
fac = slide.SequenceCompositionComparatorFactory()
comparator = fac.make(options.motif, 'sequence')
window_size = len(options.motif)
# Write output
n_written = 0
for orf in query_keys:
seq = gelscore.Sequence(prot_dict[orf])
sw = slide.SequenceWindow(seq, window_size)
# Slide window and collect results
ress = sw.slide(comparator)
# Write out results
data_outs.write("pos\taa\tscore\twindow\n")
for (xi, res) in enumerate(ress.results()):
line = "{res.position}\t{res.aa}\t{res.score}\t{res.window}\n".format(res=res)
data_outs.write(line)
data_outs.write("\n") # empty line between orfs
n_written += 1
# Write out stopping time
data_outs.write("# Run finished {}\n".format(util.timestamp()))
# Shut down output
if not options.out_fname is None: