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_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_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)
