Alignment

class pyfamsa.Alignment

An alignment, stored as a list of GappedSequence objects.

An alignment can be created from an iterable of GappedSequence that are all the same gapped size:

>>> s1 = GappedSequence(b"seq1", b"MA-WMRLLPL")
>>> s2 = GappedSequence(b"seq2", b"MALWTR-RPL")
>>> alignment = Alignment([s1, s2])

The individual rows of the alignment can be accessed using the usual indexing operation, and the alignment can be sliced to select only certain rows:

>>> alignment[0].id
b'seq1'
>>> len(alignment[:1])
1

__getitem__(key, /)

Return self[key].

__init__(sequences=())

Create a new alignment containing the provided sequences.

Parameters:

sequences (iterable of GappedSequence) – The gapped sequences to store in the alignment.

Raises:

ValueError – When the given sequences are not all of the same gapped size, thus are not forming a proper alignment.

__len__()

Return len(self).

copy()

Copy the sequence object, and return the copy.