def test_write_sequence_object(self):
fmt = FastaFormat()
with open_output(self.path, "w") as fw:
fw.write(fmt.format(Sequence("name", "CCATA")))
fw.write(fmt.format(Sequence("name2", "HELLO")))
with open(self.path) as t:
assert t.read() == '>name\nCCATA\n>name2\nHELLO\n'
def test_write_sequence_object(self):
fmt = FastaFormat()
with open_output(self.path, "w") as fw:
fw.write(fmt.format(Sequence("name", "CCATA")))
fw.write(fmt.format(Sequence("name2", "HELLO")))
with open(self.path) as t:
assert t.read() == '>name\nCCATA\n>name2\nHELLO\n'
def test_linelength(self):
fmt = FastaFormat(line_length=3)
with open_output(self.path, "w") as fw:
fw.write(fmt.format_entry("r1", "ACG"))
fw.write(fmt.format_entry("r2", "CCAT"))
fw.write(fmt.format_entry("r3", "TACCAG"))
with open(self.path) as t:
x=t.read()
print(x)
assert x == '>r1\nACG\n>r2\nCCA\nT\n>r3\nTAC\nCAG\n'
def test_linelength(self):
fmt = FastaFormat(line_length=3)
with open_output(self.path, "w") as fw:
fw.write(fmt.format_entry("r1", "ACG"))
fw.write(fmt.format_entry("r2", "CCAT"))
fw.write(fmt.format_entry("r3", "TACCAG"))
with open(self.path) as t:
x=t.read()
print(x)
assert x == '>r1\nACG\n>r2\nCCA\nT\n>r3\nTAC\nCAG\n'
def test_write_zero_length_sequence(self):
fmt = FastaFormat()
s = fmt.format_entry("name", "")
assert s == '>name\n\n', '{0!r}'.format(s)
def test_write_zero_length_sequence(self):
fmt = FastaFormat()
s = fmt.format_entry("name", "")
assert s == '>name\n\n', '{0!r}'.format(s)
