def __init__(self, msa, title='Unknown', labels=None, **kwargs):
"""*msa* must be a 2D Numpy character array. *labels* is a list of
sequence labels (or titles). *mapping* should map label or part of
label to sequence index in *msa* array. If *mapping* is not given,
one will be build from *labels*."""
self._aligned = aligned = kwargs.get('aligned', True)
msa = toChararray(msa, aligned)
numseq = msa.shape[0]
if labels and len(labels) != numseq:
raise ValueError('len(labels) must be equal to number of '
'sequences')
if labels is None:
labels = [str(i+1) for i in range(numseq)]
if PY3K:
for i, label in enumerate(labels):
if not isinstance(label, str):
labels[i] = label.decode()
self._labels = labels
mapping = kwargs.get('mapping')
self._map(mapping)
self._msa = msa
self._title = str(title) or 'Unknown'
self._split = bool(kwargs.get('split', True))
def extend(self, other):
"""Adds *other* to this MSA."""
A = self.getArray()
if isinstance(other, MSA):
B = other.getArray()
otherlabels = other._labels
elif isinstance(other, Sequence):
B = other.getArray()
B = reshape(B, (1, B.shape[0]))
otherlabels = other.getLabel(full=True)
else:
try:
B = toChararray(other, aligned=False)
numA, numB = A.shape[0], B.shape[0]
otherlabels = [str(i + 1) for i in range(numA, numA + numB)]
except:
raise ValueError('failed to add {1} to {0}'.format(
repr(self), repr(other)))
try:
AB = vstack((A, B))
except:
raise ValueError(
'failed to add {1} to {0}: shapes do not match'.format(
repr(self), repr(other)))
labels = list(self._labels)
labels.extend(otherlabels)
self._msa = AB
self._labels = labels
self._map()
def extend(self, other):
"""Adds *other* to this MSA."""
A = self.getArray()
if isinstance(other, MSA):
B = other.getArray()
otherlabels = other._labels
elif isinstance(other, Sequence):
B = other.getArray()
B = reshape(B, (1, B.shape[0]))
otherlabels = other.getLabel(full=True)
else:
try:
B = toChararray(other, aligned=False)
numA, numB = A.shape[0], B.shape[0]
otherlabels = [str(i+1) for i in range(numA, numA+numB)]
except:
raise ValueError('failed to add {1} to {0}'
.format(repr(self), repr(other)))
try:
AB = vstack((A, B))
except:
raise ValueError('failed to add {1} to {0}: shapes do not match'
.format(repr(self), repr(other)))
labels = list(self._labels)
labels.extend(otherlabels)
self._msa = AB
self._labels = labels
self._map()