def _build_repr(self, include_name):
lines = ElasticLines()
if include_name:
name_line = self.__class__.__name__
if len(self.name) > 0:
name_line += ' (%s)' % self.name
lines.add_line(name_line)
lines.add_separator()
lines.add_line(' AAs = %s' % str(self._amino_acids))
lines.add_line('Starts = %s' % str(self._starts))
base1 = 'U' * 16 + 'C' * 16 + 'A' * 16 + 'G' * 16
lines.add_line('Base1 = %s' % base1)
base2 = ('U' * 4 + 'C' * 4 + 'A' * 4 + 'G' * 4) * 4
lines.add_line('Base2 = %s' % base2)
base3 = 'UCAG' * 16
lines.add_line('Base3 = %s' % base3)
return lines.to_str()
def _build_repr(self, include_name):
lines = ElasticLines()
if include_name:
name_line = self.__class__.__name__
if len(self.name) > 0:
name_line += ' (%s)' % self.name
lines.add_line(name_line)
lines.add_separator()
lines.add_line(' AAs = %s' % str(self._amino_acids))
lines.add_line('Starts = %s' % str(self._starts))
base1 = 'U' * 16 + 'C' * 16 + 'A' * 16 + 'G' * 16
lines.add_line('Base1 = %s' % base1)
base2 = ('U' * 4 + 'C' * 4 + 'A' * 4 + 'G' * 4) * 4
lines.add_line('Base2 = %s' % base2)
base3 = 'UCAG' * 16
lines.add_line('Base3 = %s' % base3)
return lines.to_str()
def test_add_lines(self):
self.el = ElasticLines()
self.el.add_lines(['alice', 'bob', 'carol'])
self.assertEqual(self.el.to_str(), 'alice\nbob\ncarol')
def setUp(self):
self.el = ElasticLines()
class TestElasticLines(unittest.TestCase):
def setUp(self):
self.el = ElasticLines()
def test_empty(self):
self.assertEqual(self.el.to_str(), '')
def test_add_line(self):
self.el.add_line('foo')
self.assertEqual(self.el.to_str(), 'foo')
def test_add_lines(self):
self.el = ElasticLines()
self.el.add_lines(['alice', 'bob', 'carol'])
self.assertEqual(self.el.to_str(), 'alice\nbob\ncarol')
def test_add_separator(self):
self.el.add_separator()
self.assertEqual(self.el.to_str(), '')
self.el.add_line('foo')
self.assertEqual(self.el.to_str(), '---\nfoo')
self.el.add_separator()
self.el.add_lines(['bar', 'bazzzz'])
self.el.add_separator()
self.assertEqual(self.el.to_str(),
'------\nfoo\n------\nbar\nbazzzz\n------')
def build(self):
lines = ElasticLines()
cls_name = self._seq.__class__.__name__
lines.add_line(cls_name)
lines.add_separator()
if self._seq.has_metadata():
lines.add_line('Metadata:')
# Python 3 doesn't allow sorting of mixed types so we can't just
# use sorted() on the metadata keys. Sort first by type then sort
# by value within each type.
for key in self._sorted_keys_grouped_by_type(self._seq.metadata):
value = self._seq.metadata[key]
lines.add_lines(self._format_metadata_key_value(key, value))
if self._seq.has_positional_metadata():
lines.add_line('Positional metadata:')
for key in self._seq.positional_metadata.columns.values.tolist():
dtype = self._seq.positional_metadata[key].dtype
lines.add_lines(
self._format_positional_metadata_column(key, dtype))
lines.add_line('Stats:')
for label, value in self._seq._repr_stats():
lines.add_line('%s%s: %s' % (self._indent, label, value))
lines.add_separator()
num_lines, num_chars, column_width = self._find_optimal_seq_chunking()
# display entire sequence if we can, else display the first two and
# last two lines separated by ellipsis
if num_lines <= 5:
lines.add_lines(self._format_chunked_seq(
range(num_lines), num_chars, column_width))
else:
lines.add_lines(self._format_chunked_seq(
range(2), num_chars, column_width))
lines.add_line('...')
lines.add_lines(self._format_chunked_seq(
range(num_lines - 2, num_lines), num_chars, column_width))
return lines.to_str()