def test_overflow(self):
tokens = [
"ABCDEF",
"HIGJKL",
"MNOPQR",
"STUVWX",
"YZ",
]
self.assertEqual(reprnator("$START$", tokens * 4, "#END#"),
'$START$ABCDEF, HIGJKL, MNOPQR, STUVWX, YZ, ABCDEF, H'
'IGJKL, MNOPQR, STUVWX, YZ, \n ABCDEF, HIGJKL, '
'MNOPQR, STUVWX, YZ, ABCDEF, HIGJKL, MNOPQR, STUVWX, '
'YZ\n #END#')
self.assertEqual(reprnator("$START$", tokens * 3, "#END#"),
'$START$ABCDEF, HIGJKL, MNOPQR, STUVWX, YZ, ABCDEF, H'
'IGJKL, MNOPQR, STUVWX, YZ, \n ABCDEF, HIGJKL, '
'MNOPQR, STUVWX, YZ#END#')
def __repr__(self):
"""Return a string representation of the biological sequence object.
Returns
-------
str
String representation of the biological sequence object.
Notes
-----
String representation contains the class name, the first six characters
of the sequence, followed by ellipses, followed by the last six
characters of the sequence (or the full sequence without
ellipses, if the sequence is less than 21 characters long), followed by
the sequence length, followed by flags indicating whether the sequence
has metadata and/or positional metadata.
Examples
--------
>>> from skbio import Sequence
>>> s = Sequence('GGUCGUGAAGGA')
>>> s # doctest: +NORMALIZE_WHITESPACE
Sequence('GGUCGUGAAGGA', length=12, has_metadata=False,
has_positional_metadata=False)
>>> t = Sequence('ACGT')
>>> t # doctest: +NORMALIZE_WHITESPACE
Sequence('ACGT', length=4, has_metadata=False,
has_positional_metadata=False)
>>> t # doctest: +NORMALIZE_WHITESPACE
Sequence('ACGT', length=4, has_metadata=False,
has_positional_metadata=False)
>>> Sequence('GGUCGUGAAAAAAAAAAAAGGA') # doctest: +NORMALIZE_WHITESPACE
Sequence('GGUCGU ... AAAGGA', length=22, has_metadata=False,
has_positional_metadata=False)
>>> Sequence('ACGT',
... metadata={id:'seq1'}) # doctest: +NORMALIZE_WHITESPACE
Sequence('ACGT', length=4, has_metadata=True,
has_positional_metadata=False)
"""
start = self.__class__.__name__ + "("
end = ")"
tokens = []
tokens.append(self._format_str(self))
tokens.append("length=%d" % len(self))
tokens.append("has_metadata=%s" % self.has_metadata())
tokens.append("has_positional_metadata=%s" %
self.has_positional_metadata())
return reprnator(start, tokens, end)
def __repr__(self):
"""Return a string representation of the biological sequence object.
Returns
-------
str
String representation of the biological sequence object.
Notes
-----
String representation contains the class name, the first six characters
of the sequence, followed by ellipses, followed by the last six
characters of the sequence (or the full sequence without
ellipses, if the sequence is less than 21 characters long), followed by
the sequence length. If ID, description, or quality are present, they
will be included after the sequence length (and truncated in a similar
manner if they are too long).
Examples
--------
>>> from skbio import Sequence
>>> s = Sequence('GGUCGUGAAGGA')
>>> repr(s)
"Sequence('GGUCGUGAAGGA', length=12)"
>>> t = Sequence('ACGT')
>>> repr(t)
"Sequence('ACGT', length=4)"
>>> t
Sequence('ACGT', length=4)
>>> Sequence('GGUCGUGAAAAAAAAAAAAGGA')
Sequence('GGUCGU ... AAAGGA', length=22)
>>> Sequence('ACGT', id='seq1')
Sequence('ACGT', length=4, id='seq1')
"""
start = self.__class__.__name__ + "("
end = ")"
tokens = []
tokens.append(self._format_str(self))
tokens.append("length=%d" % len(self))
if self.id:
tokens.append("id=" + self._format_str(self.id))
if self.description:
tokens.append("description=" + self._format_str(self.description))
if self._has_quality():
tokens.append("quality=" + self._format_list(self.quality))
return reprnator(start, tokens, end)
def test_seperator(self):
self.assertEqual(reprnator("", list("abc"), "", separator='|'),
"a|b|c")
def test_one_line(self):
self.assertEqual(reprnator("$START$", ["bill"], "#END#"),
"$START$bill#END#")
self.assertEqual(reprnator("$START$", ["bill", "bob"], "#END#"),
"$START$bill, bob#END#")
def test_no_tokens(self):
self.assertEqual(reprnator("$START$", [], "#END#"), "$START$#END#")