skbio.alignment.Alignment¶

class skbio.alignment.Alignment(seqs, validate=False, score=None, start_end_positions=None)[source]¶

Class for storing alignments of biological sequences.

The Alignment class adds convenience methods to the SequenceCollection class to make it easy to work with alignments of biological sequences.

Parameters:

Parameters:	seqs : list of skbio.sequence.BiologicalSequence objects The skbio.sequence.BiologicalSequence objects to load into a new Alignment object. validate : bool, optional If True, runs the is_valid method after construction and raises SequenceCollectionError if `is_valid == False`. score : float, optional The score of the alignment, if applicable (usually only if the alignment was just constructed). start_end_positions : iterable of two-item tuples, optional The start and end positions of each input sequence in the alignment, if applicable (usually only if the alignment was just constructed using a local alignment algorithm). Note that these should be indexes into the unaligned sequences, though the Alignment object itself doesn’t know about these.
Raises:	skbio.util.exception.SequenceCollectionError If `validate == True` and `is_valid == False`.

seqs : list of skbio.sequence.BiologicalSequence objects

The skbio.sequence.BiologicalSequence objects to load into a new Alignment object.

validate : bool, optional

If True, runs the is_valid method after construction and raises SequenceCollectionError if is_valid == False.

score : float, optional

The score of the alignment, if applicable (usually only if the alignment was just constructed).

start_end_positions : iterable of two-item tuples, optional

The start and end positions of each input sequence in the alignment, if applicable (usually only if the alignment was just constructed using a local alignment algorithm). Note that these should be indexes into the unaligned sequences, though the Alignment object itself doesn’t know about these.

Raises:

skbio.util.exception.SequenceCollectionError

If validate == True and is_valid == False.

Notes

By definition, all of the sequences in an alignment must be of the same length. For this reason, an alignment can be thought of as a matrix of sequences (rows) by positions (columns).

Examples

>>> from skbio.alignment import Alignment
>>> from skbio.sequence import DNA
>>> sequences = [DNA('A--CCGT', id="seq1"),
...              DNA('AACCGGT', id="seq2")]
>>> a1 = Alignment(sequences)
>>> a1
<Alignment: n=2; mean +/- std length=7.00 +/- 0.00>

Methods

`__contains__`(id)	The in operator.
`__eq__`(other)	The equality operator.
`__getitem__`(index)	The indexing operator.
`__iter__`()	The iter operator.
`__len__`()	The len operator.
`__ne__`(other)	The inequality operator.
`__repr__`()	The repr method.
`__reversed__`()	The reversed method.
`__str__`()	The str method.
`degap`()	Return a new SequenceCollection with all gap characters removed.
`distances`([distance_fn])	Compute distances between all pairs of sequences
`distribution_stats`([center_f, spread_f])	Return sequence count, and center and spread of sequence lengths
`from_fasta_records`(fasta_records, ...[, ...])	Initialize a SequenceCollection object
`get_seq`(id)	Return a sequence from the SequenceCollection by its id.
`ids`()	Returns the BiologicalSequence ids
`int_map`([prefix])	Create an integer-based mapping of sequence ids
`is_empty`()	Return True if the SequenceCollection is empty
`is_valid`()	Return True if the Alignment is valid
`iter_positions`([constructor])	Generator of Alignment positions (i.e., columns)
`iteritems`()	Generator of id, sequence tuples
`k_word_frequencies`(k[, overlapping, constructor])	Return frequencies of length k words for sequences in Alignment
`lower`()	Converts all sequences to lowercase
`majority_consensus`([constructor])	Return the majority consensus sequence for the Alignment
`omit_gap_positions`(maximum_gap_frequency)	Returns Alignment with positions filtered based on gap frequency
`omit_gap_sequences`(maximum_gap_frequency)	Returns Alignment with sequences filtered based on gap frequency
`position_counters`()	Return collection.Counter object for positions in Alignment
`position_entropies`([base, ...])	Return Shannon entropy of positions in Alignment
`position_frequencies`()	Return frequencies of characters for positions in Alignment
`score`()	Returns the score of the alignment.
`sequence_count`()	Return the count of sequences in the SequenceCollection
`sequence_length`()	Return the number of positions in Alignment
`sequence_lengths`()	Return lengths of the sequences in the SequenceCollection
`start_end_positions`()	Returns the (start, end) positions for each aligned sequence.
`subalignment`([seqs_to_keep, ...])	Returns new Alignment that is a subset of the current Alignment
`toFasta`()	Return fasta-formatted string representing the SequenceCollection
`to_fasta`()	Return fasta-formatted string representing the SequenceCollection
`to_phylip`([map_labels, label_prefix])	Return phylip-formatted string representing the SequenceCollection
`upper`()	Converts all sequences to uppercase