def test_flatten(self):
"""flatten should remove one level of nesting from nested sequences
test pulled from PyCogent (http://pycogent.sourceforge.net)
"""
self.assertEqual(flatten(["aa", "bb", "cc"]), list("aabbcc"))
self.assertEqual(flatten([1, [2, 3], [[4, [5]]]]), [1, 2, 3, [4, [5]]])
def test_flatten_no_change(self):
"""flatten should not change non-nested sequences (except to list)
test pulled from PyCogent (http://pycogent.sourceforge.net)
"""
self.assertEqual(flatten("abcdef"), list("abcdef")) # test identities
self.assertEqual(flatten([]), []) # test empty sequence
self.assertEqual(flatten(""), []) # test empty string
def test_flatten(self):
"""flatten should remove one level of nesting from nested sequences
This method is ported from PyCogent (http://www.pycogent.org). PyCogent
is a GPL project, but we obtained permission from the authors of this
method to port it to the BIOM Format project (and keep it under BIOM's
BSD license).
"""
self.assertEqual(flatten(['aa', 'bb', 'cc']), list('aabbcc'))
self.assertEqual(flatten([1, [2, 3], [[4, [5]]]]), [1, 2, 3, [4, [5]]])
def test_flatten(self):
"""flatten should remove one level of nesting from nested sequences
This method is ported from PyCogent (http://www.pycogent.org). PyCogent
is a GPL project, but we obtained permission from the authors of this
method to port it to the BIOM Format project (and keep it under BIOM's
BSD license).
"""
self.assertEqual(flatten(['aa', 'bb', 'cc']), list('aabbcc'))
self.assertEqual(flatten([1, [2, 3], [[4, [5]]]]), [1, 2, 3, [4, [5]]])
def test_flatten_no_change(self):
"""flatten should not change non-nested sequences (except to list)
This method is ported from PyCogent (http://www.pycogent.org). PyCogent
is a GPL project, but we obtained permission from the authors of this
method to port it to the BIOM Format project (and keep it under BIOM's
BSD license).
"""
self.assertEqual(flatten('abcdef'), list('abcdef')) # test identities
self.assertEqual(flatten([]), []) # test empty sequence
self.assertEqual(flatten(''), []) # test empty string
def test_flatten_no_change(self):
"""flatten should not change non-nested sequences (except to list)
This method is ported from PyCogent (http://www.pycogent.org). PyCogent
is a GPL project, but we obtained permission from the authors of this
method to port it to the BIOM Format project (and keep it under BIOM's
BSD license).
"""
self.assertEqual(flatten('abcdef'), list('abcdef')) # test identities
self.assertEqual(flatten([]), []) # test empty sequence
self.assertEqual(flatten(''), []) # test empty string
def list_dict_to_sparsemat(data, dtype=float):
"""Takes a list of dict {(0,col):val} and creates a SparseMat"""
if isinstance(data[0], SparseMat):
if data[0].shape[0] > data[0].shape[1]:
is_col = True
n_cols = len(data)
n_rows = data[0].shape[0]
else:
is_col = False
n_rows = len(data)
n_cols = data[0].shape[1]
else:
all_keys = flatten([d.keys() for d in data])
n_rows = max(all_keys, key=itemgetter(0))[0] + 1
n_cols = max(all_keys, key=itemgetter(1))[1] + 1
if n_rows > n_cols:
is_col = True
n_cols = len(data)
else:
is_col = False
n_rows = len(data)
mat = SparseMat(n_rows, n_cols, dtype=dtype)
for row_idx,row in enumerate(data):
for (foo,col_idx),val in row.items():
if is_col:
mat[foo,row_idx] = val
else:
mat[row_idx,col_idx] = val
return mat
def list_dict_to_csmat(data, dtype=float):
"""Takes a list of dict {(0,col):val} and creates a CSMat"""
if isinstance(data[0], CSMat):
if data[0].shape[0] > data[0].shape[1]:
is_col = True
n_cols = len(data)
n_rows = data[0].shape[0]
else:
is_col = False
n_rows = len(data)
n_cols = data[0].shape[1]
else:
all_keys = flatten([d.keys() for d in data])
n_rows = max(all_keys, key=itemgetter(0))[0] + 1
n_cols = max(all_keys, key=itemgetter(1))[1] + 1
if n_rows > n_cols:
is_col = True
n_cols = len(data)
else:
is_col = False
n_rows = len(data)
mat = CSMat(n_rows, n_cols, dtype=dtype)
rows = []
cols = []
vals = []
for row_idx,row in enumerate(data):
for (foo,col_idx),val in row.items():
if is_col:
# transpose
rows.append(foo)
cols.append(row_idx)
vals.append(val)
else:
rows.append(row_idx)
cols.append(col_idx)
vals.append(val)
mat.bulkCOOUpdate(rows, cols, vals)
return mat
def list_dict_to_scipy(data, dtype=float):
"""Takes a list of dict {(row,col):val} and creates a
``ScipySparseMat``.
"""
if isinstance(data[0], ScipySparseMat):
if data[0].shape[0] > data[0].shape[1]:
is_col = True
n_cols = len(data)
n_rows = data[0].shape[0]
else:
is_col = False
n_rows = len(data)
n_cols = data[0].shape[1]
else:
all_keys = flatten([d.keys() for d in data])
n_rows = max(all_keys, key=itemgetter(0))[0] + 1
n_cols = max(all_keys, key=itemgetter(1))[1] + 1
if n_rows > n_cols:
is_col = True
n_cols = len(data)
else:
is_col = False
n_rows = len(data)
rows = []
cols = []
vals = []
for row_idx, row in enumerate(data):
for (foo, col_idx), val in row.items():
if is_col:
# transpose
rows.append(foo)
cols.append(row_idx)
vals.append(val)
else:
rows.append(row_idx)
cols.append(col_idx)
vals.append(val)
return ScipySparseMat(n_rows, n_cols, dtype=dtype,
data=(vals, (rows, cols)))