def test_len(self):
"""returns the length of the flowgram"""
f = Flowgram('0.5 1.0 4.0 0.0')
self.assertEqual(len(f), 4)
f = Flowgram()
self.assertEqual(len(f), 0)
def test_writeToFile(self):
"""FlowgramCollection.writeToFile should write in correct format"""
a = [
Flowgram('0.5 1.0 4.0 0.0 1.5 0.0 0.0 2.0',
Name='a',
header_info={
'Bases': 'TACCCCTTGG',
'Name Length': '14'
}),
Flowgram('1.5 1.0 0.0 0.0 2.5 1.0 2.0 1.0',
Name='b',
header_info={
'Bases': 'TTATTTACCG',
'Name Length': '14'
})
]
f = FlowgramCollection(a, header_info={'Flow Chars': 'TACG'})
fn = mktemp(suffix='.sff')
f.writeToFile(fn)
result = open(fn, 'U').read()
self.assertEqual(
result,
"""Common Header:\n Flow Chars:\tTACG\n\n>a\n Name Length:\t14\nBases:\tTACCCCTTGG\nFlowgram:\t0.5\t1.0\t4.0\t0.0\t1.5\t0.0\t0.0\t2.0\n\n>b\n Name Length:\t14\nBases:\tTTATTTACCG\nFlowgram:\t1.5\t1.0\t0.0\t0.0\t2.5\t1.0\t2.0\t1.0\n"""
)
remove(fn)
def test_append_to_flowgram_file(self):
"""append_to_flowgram_file appends a flowgram to a flowgram file."""
fh, tmp_filename = init_flowgram_file(n=100, l=400)
self.assert_(exists(tmp_filename))
self.tmp_filename = tmp_filename
flow1 = Flowgram("0 1.2 2.1 3.4 0.02 0.01 1.02 0.08")
append_to_flowgram_file("test_id", flow1, fh)
flow2 = Flowgram('0.5 1.0 4.1 0.0 0.0 1.23 0.0 3.1',
Name='a',
floworder="TACG",
header_info={
'Bases': 'TACCCCAGGG',
'Clip Qual Right': 7,
'Flow Indexes': "1\t2\t3\t3\t3\t3\t6\t8\t8\t8"
})
append_to_flowgram_file("test_id2", flow2, fh, trim=True)
# close and re-open to read from start, seek might work as well here...
fh.close()
fh = open(tmp_filename)
result_file_content = list(fh)
self.assertEqual(result_file_content, [
"100 400\n", "test_id 8 0.0 1.2 2.1 3.4 0.02 0.01 1.02 0.08\n",
"test_id2 6 0.5 1.0 4.1 0.0 0.0 1.23\n"
])
def test_hash(self):
"""__hash__ behaves like the flowgram string for dict lookup."""
f = Flowgram('0.5 1.0 4.0 0.0', floworder="TACG")
self.assertEqual(hash(f), hash('0.5 1.0 4.0 0.0'))
f = Flowgram()
self.assertEqual(hash(f), hash(''))
def test_str(self):
"""FlowgramCollection __str__ should return sff format"""
a = [Flowgram('0.5 1.0 4.0 0.0 1.5 0.0 0.0 2.0', Name='a',
header_info = {'Bases':'TACCCCTTGG','Name Length':'14'}),
Flowgram('1.5 1.0 0.0 0.0 2.5 1.0 2.0 1.0', Name = 'b',
header_info = {'Bases':'TTATTTACCG','Name Length':'14'})]
f = FlowgramCollection(a, header_info = {'Flow Chars':'TACG'})
self.assertEqual(str(f), """Common Header:\n Flow Chars:\tTACG\n\n>a\n Name Length:\t14\nBases:\tTACCCCTTGG\nFlowgram:\t0.5\t1.0\t4.0\t0.0\t1.5\t0.0\t0.0\t2.0\n\n>b\n Name Length:\t14\nBases:\tTTATTTACCG\nFlowgram:\t1.5\t1.0\t0.0\t0.0\t2.5\t1.0\t2.0\t1.0\n""")
def test_createCommonHeader(self):
"""create_commor_header should return lines for sff common header"""
a = [Flowgram('0.5 1.0 4.0 0.0 1.5 0.0 0.0 2.0', Name='a',
header_info = {'Bases':'TACCCCTTGG','Name Length':'14'}),
Flowgram('1.5 1.0 0.0 0.0 2.5 1.0 2.0 1.0', Name = 'b',
header_info = {'Bases':'TTATTTACCG','Name Length':'14'})]
f = FlowgramCollection(a, header_info = {'Flow Chars':'TACG'})
self.assertEqual('\n'.join(f.createCommonHeader()),
"""Common Header:\n Flow Chars:\tTACG""")
def test_within_length(self):
"""within_length checks whether a flowgram is within a given length."""
flow1 = Flowgram("0 1.2 2.1 3.4 0.02 0.01 1.02 0.08") # len 7
flow2 = Flowgram('0.5 1.0 4.1 0.0 0.0 1.23 0.0 3.1') # len 10
self.assertTrue(within_length(flow1, 0,10))
self.assertFalse(within_length(flow1, 10,20))
self.assertFalse(within_length(flow2, 0,5))
self.assertTrue(within_length(flow2, 5,20))
self.assertTrue(within_length(flow2, 5,11))
def test_cmpSeqToString(self):
"""Sequence should compare equal to same string."""
f = Flowgram('0.5 1.0 4.0 0.0',
Name='a',
floworder="TACG",
header_info={'Bases': 'TACCCC'})
self.assertTrue(f.cmpSeqToString('TACCCC'))
self.assertFalse(f.cmpSeqToString('TACCC'))
f = Flowgram('0.5 1.0 4.0 0.0', floworder="TACG")
self.assertTrue(f.cmpSeqToString('TACCCC'))
self.assertFalse(f.cmpSeqToString('TACCC'))
def test_cmp(self):
"""_cmp_ should compare the flowgram strings."""
f1 = Flowgram(['1 2 3 4'])
f2 = Flowgram(['2 2 3 4'])
self.assertNotEqual(f1, f2)
self.assertEqual(f1, f1)
#works also with string
self.assertNotEqual(f1, "1 2 3 5")
self.assertEqual(f1, "1 2 3 4")
self.assertNotEqual(f1, "")
def test_init_flow(self):
"""FlowgramCollection init from list of flowgrams should use indices
as keys"""
f1 = Flowgram('0.0 1.1 3.0 1.0')
f2 = Flowgram('0.5 1.0 4.0 0.0')
flows = [f1,f2]
a = self.Class(flows)
self.assertEqual(len(a.NamedFlows), 2)
self.assertEqual(a.NamedFlows['seq_0'], '0.0 1.1 3.0 1.0')
self.assertEqual(a.NamedFlows['seq_1'], '0.5 1.0 4.0 0.0')
self.assertEqual(a.Names, ['seq_0','seq_1'])
self.assertEqual(list(a.Flows), ['0.0 1.1 3.0 1.0','0.5 1.0 4.0 0.0'])
def test_flows_from_dict(self):
"""flows_from_dict should init from dictionary"""
c = {'a':'0.0 1.1 3.0 1.0','b':'0.5 1.0 4.0 0.0'}
obs_a, obs_labels, obs_info = flows_from_dict(c)
self.assertEqual(map(str,obs_a), ['0.0 1.1 3.0 1.0','0.5 1.0 4.0 0.0'])
self.assertEqual(obs_labels, ['a','b'])
self.assertEqual(obs_info, [None,None])
c ={'a':Flowgram('0.0 1.1 3.0 1.0'),'b':Flowgram('0.5 1.0 4.0 0.0')}
obs_a, obs_labels, obs_info = flows_from_dict(c)
self.assertEqual(map(str,obs_a), ['0.0\t1.1\t3.0\t1.0','0.5\t1.0\t4.0\t0.0'])
self.assertEqual(obs_labels, ['a','b'])
self.assertEqual(obs_info, [None,None])
def test_cmp_flow_to_string(self):
"""Sequence should compare equal to same string."""
f = Flowgram('0.5 1.0 4.0 0.0',
Name='a',
floworder="TACG",
header_info={'Bases': 'TACCCC'})
self.assertEqual(f, '0.5 1.0 4.0 0.0')
self.assertNotEqual(f, '0.5 1.0 4.0')
f2 = Flowgram('0.5 1.0 4.0 0.0',
Name='a',
floworder="TACG",
header_info={'Bases': 'TACCCC'})
self.assertEqual(f, f2)
def test_flows_from_kv_pairs(self):
"""seqs_from_kv_pairs should initialize from key-value pairs"""
c = [['a','0.0 1.1 3.0 1.0'],['b','0.5 1.0 4.0 0.0']]
obs_a, obs_labels, obs_info = flows_from_kv_pairs(c)
self.assertEqual(map(str,obs_a), ['0.0 1.1 3.0 1.0','0.5 1.0 4.0 0.0'])
self.assertEqual(obs_labels, ['a','b'])
self.assertEqual(obs_info, [None,None])
c =[['a',Flowgram('0.0 1.1 3.0 1.0')],['b',Flowgram('0.5 1.0 4.0 0.0')]]
obs_a, obs_labels, obs_info = flows_from_kv_pairs(c)
self.assertEqual(map(str,obs_a), ['0.0\t1.1\t3.0\t1.0','0.5\t1.0\t4.0\t0.0'])
self.assertEqual(obs_labels, ['a','b'])
self.assertEqual(obs_info, [None,None])
def test_setBases(self):
"""FlowgramCollection setBases should set Bases property correctly"""
f = self.Class([Flowgram('0.5 1.0 4.0 0.0 1.5 0.0 0.0 2.0', Name='a',
header_info = {'Bases':'TACCCCTTGG'}),
Flowgram('0.0 1.0 0.0 0.0 2.0 1.0 2.0 2.0', Name='b',
header_info = {'Bases':'ATTACCGG'}),
Flowgram('1.5 1.0 2.0 0.0 1.5 0.0 0.0 2.0', Name='c',
header_info = {'Bases':'TTACCTTGG'})],
header_info = {'Flow Chars':'TACG'})
f.setBases()
for i,b in zip(f,['TACCCCTTGG','ATTACCGG','TTACCTTGG']):
self.assertEqual(i.Bases,b)
def test_check_ambigous(self):
"""check_ambigous detects stretches of ambigous Flows."""
flow0 = Flowgram("")
flow1 = Flowgram("0 1.2 2.1 3.4 0.02 0.01 1.02 0.08 0.5 1.0 4.1 0.0 0.0 1.23 0.0 3.1")
flow2 = Flowgram("0 1.2 2.1 3.4 0.02 0.01 1.02 0.08 0.5 1.0 4.1 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.23 0.0 3.1")
flow3 = Flowgram("0 1.2 2.1 3.4 0.02 0.0 0.0 0.01 1.02 0.08 0.5 1.0 4.1 0.0 0.0 0.0 0.0 1.23 0.0 3.1")
self.assertEqual(check_ambigous(flow0, 4), False)
self.assertEqual(check_ambigous(flow1, 4), False)
self.assertEqual(check_ambigous(flow2, 4), True)
self.assertEqual(check_ambigous(flow2, 7), True)
self.assertEqual(check_ambigous(flow2, 8), False)
self.assertEqual(check_ambigous(flow3, 3), True)
self.assertEqual(check_ambigous(flow3, 4), False)
def test_guess_input_type(self):
""" _guess_input_type should figure out data type correctly"""
git = self.unordered._guess_input_type
self.assertEqual(git(self.unordered), 'flowcoll')
self.assertEqual(git(['0.0 1.1 3.0 1.0','0.5 1.0 4.0 0.0']), 'generic')
self.assertEqual(git([Flowgram('0.0 1.1 3.0 1.0'),
Flowgram('0.5 1.0 4.0 0.0')]), 'generic')
self.assertEqual(git([[1,2],[4,5]]), 'kv_pairs') #precedence over generic
self.assertEqual(git([('a',Flowgram('0.0 1.1 3.0 1.0')),
('b',Flowgram('0.5 1.0 4.0 0.0'))]), 'kv_pairs')
self.assertEqual(git([[1,2,3],[4,5,6]]), 'generic')
self.assertEqual(git(array([[1,2,3],[4,5,6]])), 'array')
self.assertEqual(git({'a':'0.0 1.1 3.0 1.0'}), 'dict')
self.assertEqual(git({'a':Flowgram('0.0 1.1 3.0 1.0')}), 'dict')
self.assertEqual(git([]), 'empty')
self.assertEqual(git('Common Header'), 'sff')
def test_flows_from_generic(self):
"""flows_from_flow should initialize from list of flowgram objects"""
c = Flowgram('0.0 1.1 3.0 1.0', Name='a')
b = Flowgram('0.5 1.0 4.0 0.0', Name = 'b')
obs_a, obs_labels, obs_info = flows_from_generic([c,b])
self.assertEqual(map(str,obs_a), ['0.0\t1.1\t3.0\t1.0',
'0.5\t1.0\t4.0\t0.0'])
self.assertEqual(obs_labels, ['a','b'])
self.assertEqual(obs_info, [None,None])
f = ['0.0 1.1 3.0 1.0','0.5 1.0 4.0 0.0']
obs_a, obs_labels, obs_info = flows_from_generic(f)
self.assertEqual(map(str,obs_a), ['0.0 1.1 3.0 1.0',
'0.5 1.0 4.0 0.0'])
self.assertEqual(obs_labels, [None,None])
self.assertEqual(obs_info, [None,None])
def _average_flowgrams(mapping, flowgrams, sample_keys):
"""average flowgrams according to cluster mapping.
mapping: a dictionary of lists as cluster mapping
flowgrams: an iterable flowgram source, all flowgram ids from this source must be in the mapping
sample_keys: the keys that should be averaged over for each cluster.
"""
flows = defaultdict(list) # accumulates flowgram for each key until sample for this key is empty
invert_map = invert_mapping(mapping)
for f in flowgrams:
key = invert_map[f.Name]
samples = sample_keys[key]
if (f.Name in samples):
flows[key].append(f.flowgram)
samples.remove(f.Name)
if (len(samples)==0):
#we gathered all sampled flowgrams for this cluster,
#now average
ave_flowgram = build_averaged_flowgram(flows[key])
ave_f = Flowgram(ave_flowgram, Name=key)
del(flows[key])
yield ave_f, key
def test_cmpByName(self):
"""Flowgrams should be the same if name, bases, or to_seqs are equal"""
f = Flowgram('0.5 1.0 4.0 0.0',
Name='a',
floworder="TACG",
header_info={'Bases': 'TACCCC'})
f2 = Flowgram('0.5 1.0 4.0 0.0',
Name='a',
floworder="TACG",
header_info={'Bases': 'TACCCC'})
self.assertEqual(f.cmpByName(f2), 0)
self.assertEqual(f.cmpByName(f), 0)
f2 = Flowgram('0.5 1.0 4.0 0.0',
Name='b',
floworder="TACG",
header_info={'Bases': 'TACCCC'})
self.assertNotEqual(f.cmpByName(f2), 0)
def test_contains(self):
"""Flowgram contains should return correct result"""
f = Flowgram('0.5 1.0 4.0 0.0',
Name='a',
floworder="TACG",
header_info={'Bases': 'TACCCC'})
assert '0.5' in f
assert '0.5 1.0' in f
assert '2.0' not in f
assert '5.0' not in f
def _sff_parser(handle, header):
for s in handle:
t = split_summary(s)
flowgram = t["Flowgram"]
del t["Flowgram"]
flowgram = Flowgram(flowgram,
Name=t["Name"],
KeySeq=header["Key Sequence"],
floworder=header["Flow Chars"],
header_info=t)
yield flowgram
def test_createFlowHeader(self):
"""header_info dict turned into flowgram header"""
f = Flowgram('0.5 1.0 4.0 0.0 1.5 0.0 0.0 2.0',
Name='a',
header_info={
'Bases': 'TACCCCTTGG',
'Name Length': '14'
})
self.assertEqual(
f.createFlowHeader(),
""">a\n Name Length:\t14\nBases:\tTACCCCTTGG\nFlowgram:\t0.5\t1.0\t4.0\t0.0\t1.5\t0.0\t0.0\t2.0\n"""
)
def test_init_data(self):
"""Flowgram init with data should set data in correct location"""
f = Flowgram('0.5 1.0 4.0 0.0',
Name='a',
KeySeq="ATCG",
floworder="TACG",
header_info={'Bases': 'TACCCC'})
self.assertEqual(f._flowgram, '0.5 1.0 4.0 0.0')
self.assertEqual(f.flowgram, [0.5, 1.0, 4.0, 0.0])
self.assertEqual(f.Name, 'a')
self.assertEqual(f.keySeq, "ATCG")
self.assertEqual(f.floworder, "TACG")
self.assertEqual(f.Bases, 'TACCCC')
self.assertEqual(f.header_info, {'Bases': 'TACCCC'})
f = Flowgram([0.5, 1.0, 4.0, 0.0],
Name='a',
KeySeq="ATCG",
floworder="TACG",
header_info={'Bases': 'TACCCC'})
self.assertEqual(f._flowgram, '0.5 1.0 4.0 0.0')
self.assertEqual(f.flowgram, [0.5, 1.0, 4.0, 0.0])
def test_toSequenceCollection(self):
"""toSequenceCollection should return sequence collection from flows"""
f = self.Class( [ '0.5 1.0 4.0 0.0 1.5 0.0 0.0 2.0',
'1.5 1.0 0.0 0.0 2.5 1.0 2.0 1.0',
'2.5 0.0 4.0 0.0 0.5 1.0 0.0 1.0',
'0.0 1.0 0.0 3.0 1.5 1.0 1.0 2.0'
], header_info = {'Flow Chars':'TACG'})
s = f.toSequenceCollection()
assert isinstance(s,SequenceCollection)
for i,j in zip(s.iterSeqs(),['TACCCCTTGG','TTATTTACCG','TTTCCCCTAG',
'AGGGTTACGG']):
self.assertEqual(i,j)
a = [Flowgram('0.5 1.0 4.0 0.0 1.5 0.0 0.0 2.0', Name='a',
header_info = {'Bases':'TACTTGG','Name Length':'14'}),
Flowgram('1.5 1.0 0.0 0.0 2.5 1.0 2.0 1.0', Name = 'b',
header_info = {'Bases':'TTATTTG','Name Length':'14'})]
f = self.Class(a)
s = f.toSequenceCollection(Bases = True)
assert isinstance(s,SequenceCollection)
for i,j in zip(s.iterSeqs(),['TACTTGG','TTATTTG']):
self.assertEqual(i,j)
def test_toFasta(self):
"""Flowgram toFasta() should return Fasta-format string"""
even = '0.5 1.0 4.0 0.0'
odd = '0.5 1.0 4.0 1.0'
even_f = Flowgram(even, Name='even', floworder="TACG")
odd_f = Flowgram(odd, Name='odd', floworder="TACG")
self.assertEqual(even_f.toFasta(), '>even\nTACCCC')
#set line wrap to small number so we can test that it works
self.assertEqual(even_f.toFasta(LineWrap=2), '>even\nTA\nCC\nCC')
self.assertEqual(odd_f.toFasta(LineWrap=2), '>odd\nTA\nCC\nCC\nG')
even_f = Flowgram(even,
Name='even',
floworder="TACG",
header_info={'Bases': 'TACCCG'})
odd_f = Flowgram(odd,
Name='odd',
floworder="TACG",
header_info={'Bases': 'TACCCGG'})
self.assertEqual(even_f.toFasta(), '>even\nTACCCG')
#set line wrap to small number so we can test that it works
self.assertEqual(even_f.toFasta(LineWrap=2), '>even\nTA\nCC\nCG')
self.assertEqual(odd_f.toFasta(LineWrap=2), '>odd\nTA\nCC\nCG\nG')
def test_average_flowgrams(self):
"""_average_flowgrams computes an averaged flowgram for each cluster."""
fc = FlowgramCollection({
'a': '1.0 0.0 0.0 1.0 1.0 1.2 1.2 0.8',
'b': '1.2 1.0 0.0 0.8 1.2 2.4 1.0 0.0'
})
#return the centroid unmodified if sample_mapping = 1
actual = list(_average_flowgrams({'a': 'b'}, fc, {'a': ['a']}))
self.assertEqual(actual, [(fc.getFlow('a'), 'a')])
actual = list(_average_flowgrams({'a': 'b'}, fc, {'a': ['a', 'b']}))
self.assertEqual(
actual, [(Flowgram(['1.1 0.5 0.0 0.9 1.1 1.8 1.1 0.4']), 'a')])
def test_toSeq(self):
"""toSeq should Translate flowgram to sequence"""
f = Flowgram('0.5 1.0 4.0 0.0',
Name='a',
floworder="TACG",
header_info={'Bases': 'TACCCG'})
self.assertEqual(f.toSeq(), 'TACCCG')
self.assertEqual(isinstance(f.toSeq(), Sequence), True)
self.assertEqual(f.toSeq(Bases=False), 'TACCCC')
f = Flowgram('0.5 1.0 4.0 0.0 0.0 1.23 0.0 6.1',
Name='a',
floworder="TACG",
header_info={'Bases': 'TACCCG'})
self.assertEqual(f.toSeq(), 'TACCCG')
self.assertEqual(f.toSeq(Bases=False), 'TACCCCAGGGGGG')
f = Flowgram('0.5 1.0 4.0 0.0',
Name='a',
floworder="TACG",
header_info={})
self.assertEqual(f.toSeq(), 'TACCCC')
self.assertEqual(isinstance(f.toSeq(), Sequence), True)
self.assertEqual(f.toSeq(Bases=False), 'TACCCC')
f = Flowgram('0.5 1.0 4.0 0.0 0.0 1.23 0.0 6.1',
Name='a',
floworder="TACG",
header_info={})
self.assertEqual(f.toSeq(Bases=True), 'TACCCCAGGGGGG')
f = Flowgram('0.4 0.0 0.0 0.0 0.0 1.23 0.0 1.1',
Name='a',
floworder="TACG",
header_info={})
self.assertEqual(f.toSeq(), 'NAG')
def parse_sff(lines):
"""Creates list of flowgram objects from a SFF file
"""
head = get_header_info(lines)
summaries = get_all_summaries(lines)
flows = []
for s in summaries:
t = split_summary(s)
flowgram = t["Flowgram"]
del t["Flowgram"]
flows.append(
Flowgram(flowgram,
Name=t["Name"],
floworder=head["Flow Chars"],
header_info=t))
return flows, head
def test_getQualityTrimmedFlowgram(self):
"""getQualityTrimmedFlowgram trims the flowgram correctly"""
f = Flowgram('0.5 1.0 4.1 0.0 0.0 1.23 0.0 3.1',
Name='a',
floworder="TACG",
header_info={
'Bases': 'TACCCCAGGG',
'Clip Qual Right': 7,
'Flow Indexes': "1\t2\t3\t3\t3\t3\t6\t8\t8\t8"
})
trimmed = f.getQualityTrimmedFlowgram()
self.assertEqual(trimmed.toSeq(), "TACCCCA")
self.assertEqual(str(trimmed), "0.5\t1.0\t4.1\t0.0\t0.0\t1.23")
# tests on real data
flow1 = self.flows[0]
flow2 = self.flows[1]
flow1_trimmed = flow1.getQualityTrimmedFlowgram()
self.assertEqual(
str(flow1_trimmed),
"1.06 0.08 1.04 0.08 0.05 0.94 0.10 2.01 0.10 0.07 0.96 0.09 1.04 1.96 1.07 0.10 1.01 0.13 0.08 1.01 1.06 1.83 2.89 0.18 0.96 0.13 0.99 0.11 1.94 0.12 0.13 1.92 0.21 0.07 0.94 0.17 0.03 0.97 2.76 0.15 0.05 1.02 1.14 0.10 0.98 2.54 1.13 0.96 0.15 0.21 1.90 0.16 0.07 1.78 0.22 0.07 0.93 0.22 0.97 0.08 2.02 0.15 0.19 1.02 0.19 0.09 1.02 0.17 0.99 0.09 0.18 1.84 0.16 0.91 0.10 1.10 1.00 0.20 0.09 1.11 3.01 1.07 1.98 0.14 0.22 1.09 0.17 1.99 0.15 0.20 0.92 0.17 0.07 1.01 2.96 0.15 0.07 1.06 0.20 1.00 0.10 0.12 1.00 0.15 0.08 1.90 0.19 0.10 0.99 0.18 0.09 0.99 1.08 0.15 0.07 1.06 0.14 1.84 0.13 0.11 0.95 1.05 0.13 1.04 1.10 0.18 0.94 0.14 0.10 0.97"
)
self.assertEqual(
flow1_trimmed.Bases,
"tcagGCTAACTGTAACCCTCTTGGCACCCACTAAACGCCAATCTTGCTGGAGTGTTTACCAGGCACCCAGCAATGTGAATAGTCA"
)
flow2_trimmed = flow2.getQualityTrimmedFlowgram()
self.assertEqual(
str(flow2_trimmed),
"1.04 0.00 1.01 0.00 0.00 1.00 0.00 1.00 0.00 1.05 0.00 0.91 0.10 1.07 0.95 1.01 0.00 0.06 0.93 0.02 0.03 1.06 1.18 0.09 1.00 0.05 0.90 0.11 0.07 1.99 0.11 0.02 1.96 1.04 0.13 0.01 2.83 0.10 1.97 0.06 0.11 1.04 0.13 0.03 0.98 1.15 0.07 1.00 0.07 0.08 0.98 0.11 1.92 0.05 0.04 2.96 1.02 1.02 0.04 0.93 1.00 0.13 0.04 1.00 1.03 0.08 0.97 0.13 0.11 1.88 0.09 0.05 1.02 1.89 0.07 0.11 0.98 0.05 0.07 1.01 0.08 0.05 1.01 0.13 1.00 0.07 0.10 1.04 0.10 0.04 0.98 0.12 1.03 0.96 0.11 0.07 1.00 0.09 0.03 1.03 0.11 1.95 1.06 0.13 0.05 1.00 0.13 0.11 1.00 0.09 0.03 2.89 0.08 0.95 0.09 1.03 1.02 1.05 1.07 0.08 0.12 2.81 0.08 0.08 1.00 1.07 0.07 0.05 1.86 0.12 0.98 0.06 2.00 0.11 1.02 0.11 0.08 1.88 0.13 1.03 0.13 0.98 0.15 0.11 1.03 1.03 1.04 0.18 0.98 0.13 0.15 1.04 0.11 1.01 0.13 0.06 1.01 0.06 1.02 0.08 0.99 0.14 0.99 0.09 0.05 1.09 0.04 0.07 2.96 0.09 2.03 0.13 2.96 1.13 0.08 1.03 0.07 0.99 0.11 0.05 1.05 1.04 0.09 0.07 1.00 1.03 0.09 0.06 1.06 1.04 2.94 0.18 0.06 0.93 0.10 1.10 0.11 2.02 0.17 1.00 1.03 0.06 0.11 0.96 0.04 3.00 0.11 0.07 1.99 0.10 2.03 0.12 0.97 0.16 0.01 2.09 0.14 1.04 0.16 0.06 1.03 0.14 1.12 0.12 0.05 0.96 1.01 0.10 0.14 0.94 0.03 0.12 1.10 0.92 0.09 1.10 1.04 1.02 0.12 0.97 2.00 0.15 1.08 0.04 1.03 1.04 0.03 0.09 5.16 1.02 0.09 0.13 2.66 0.09 0.05 1.06 0.07 0.89 0.05 0.12 1.10 0.16 0.06 1.01 0.13 1.00 0.14 0.98 0.09 2.92 1.28 0.03 2.95 0.98 0.16 0.08 0.95 0.96 1.09 0.08 1.07 1.01 0.16 0.06 4.52 0.12 1.03 0.07 0.09 1.03 0.14 0.03 1.01 1.99"
)
self.assertEqual(
flow2_trimmed.Bases,
"tcagAGACGCACTCAATTATTTCCATAGCTTGGGTAGTGTCAATAATGCTGCTATGAACATGGGAGTACAAATATTCTTCAAGATACTGATCTCATTTCCTTTAGATATATACCCAGAAGTGAAATTCCTGGATCACATAGTAGTTCTATTTTTATTTGATGAGAAACTTTATACTATTTTTCATAA"
)
flowgram = Flowgram("0.99 0.00 0.99 0.00 0.00 1.02 0.00 1.00 1.00 1.12\t\t"+\
"0.01 0.01 1.89 0.01 0.95 0.95 0.97 0.00 0.02 0.98\t"+\
"0.97 0.00 0.97 0.05 0.01 1.06 0.03 0.97 0.00 0.03\t"+\
"0.97 0.02 0.00 1.09 0.02 0.01 0.96 0.00 0.00 1.01\t"+\
"0.04 0.00 0.99 0.06 0.97 0.00 0.09 0.97 0.04 0.00\t"+\
"1.94 0.09 1.02 0.00 2.86 1.02 1.00 1.11 0.10 1.97\t"+\
"0.12 0.98 0.01 0.99 2.90 0.03 0.04 1.93 0.15 1.02\t"+\
"1.95 1.00 1.02 0.00 0.12 1.00 0.97 0.00 1.00 0.06\t"+\
"0.97 0.00 0.96 0.05 0.10 1.03 0.12 0.99 1.98 0.09\t"+\
"1.99 0.08 0.13 2.10 0.14 0.05 1.00 0.10 0.00 1.00\t"+\
"1.00 0.00 0.07 4.82 0.10 1.04 2.05 0.00 2.01 0.04\t"+\
"1.96 0.08 0.93 0.00 0.93 0.03 0.99 0.02 1.01 0.06\t"+\
"0.09 1.04 0.14 1.06 0.07 2.04 3.49 0.15 1.02 0.80\t"+\
"0.23 0.07 1.07 0.17 1.91 0.07 0.18 1.00 0.32 0.07\t"+\
"0.97 0.11 0.96 0.96 0.14 1.96 0.19 2.01 2.84 0.28\t"+\
"0.08 2.03 1.32 0.06 0.05 1.10 0.17 0.88 0.09 0.95\t"+\
"0.14 0.13 1.85 1.07 1.78 0.89 1.94 0.19 1.09 0.14\t"+\
"1.09 0.13 0.13 0.86 1.85 0.07 0.09 1.97 1.20 0.08\t"+\
"0.95 0.23 0.09 0.94 0.16 0.11 1.92 0.12 0.89 1.95\t"+\
"0.21 0.12 0.97 0.14 0.16 1.86 0.12 1.89 1.00 1.07\t"+\
"0.06 0.16 1.05 0.11 0.06 0.95 0.12 0.13 1.01 0.15\t"+\
"3.79 0.14 0.15 0.98 0.40 0.11 1.00 0.19 1.01 1.09\t"+\
"0.12 0.94 0.11 0.15 1.00 2.04 2.03 0.95 0.06 3.05\t"+\
"0.22 0.08 1.82 0.21 1.02 0.09 2.88 1.88 0.15 0.07\t"+\
"1.05 1.89 0.08 0.06 1.87 2.87 1.87 0.06 0.15 1.15\t"+\
"0.25 0.08 0.96 0.12 0.06 0.95 0.09 0.13 1.05 1.95\t"+\
"3.81 1.02 0.13 0.17 2.14 1.08 0.19 0.13 1.08 1.01\t"+\
"1.99 0.11 0.18 1.06 0.17 0.04 0.98 0.08 1.01 2.86\t"+\
"1.06 0.96 0.10 0.22 1.99 2.04 0.14 0.00 0.97 0.16\t"+\
"0.95 0.07 2.75 0.02 0.98 0.12 2.94 0.00 0.99 1.03\t"+\
"0.26 2.89 0.15 1.87 0.10 0.15 0.98 0.17 1.07 0.92\t"+\
"0.00 0.09 1.08 0.16 3.78 1.01 0.07 0.87 0.22 0.98\t"+\
"1.97 1.09 0.08 0.17 1.08 0.03 0.97 2.04 0.18 0.14\t"+\
"1.03 0.03 0.00 1.16 0.12 1.81 2.06 0.18 0.17 2.06\t"+\
"0.14 0.85 0.21 0.12 1.01 1.05 1.05 0.94 0.99 0.11\t"+\
"0.15 1.08 2.00 1.02 0.99 0.13 1.07 0.13 0.98 0.16\t"+\
"0.09 0.99 3.00 1.05 1.02 0.02 0.10 0.93 0.11 0.09\t"+\
"0.81 0.97 0.13 0.05 2.04 1.93 1.12 0.04 0.93 0.93\t"+\
"0.11 0.06 1.96 0.06 0.09 1.14 0.15 0.06 1.08 0.06\t"+\
"0.94 0.11 0.00 0.88 1.11 0.10 2.08 1.05 0.15 0.09")
