biotite.sequence.align.Alignment

class biotite.sequence.align.Alignment(sequences, trace, score=None)[source]

Bases: object

An Alignment object stores information about which symbols of n sequences are aligned to each other and it stores the corresponding alignment score.

Instead of saving a list of aligned symbols, this class saves the original n sequences, that were aligned, and a so called trace, which indicate the aligned symbols of these sequences. The trace is a (m x n) ndarray with alignment length m and sequence count n. Each element of the trace is the index in the corresponding sequence. A gap is represented by the value -1.

Furthermore this class provides multiple utility functions for conversion into strings in order to make the alignment human readable.

Unless an Alignment object is the result of an multiple sequence alignment, the object will contain only two sequences.

All attributes of this class are publicly accessible.

Parameters:
sequenceslist

A list of aligned sequences.

tracendarray, dtype=int, shape=(n,m)

The alignment trace.

scoreint, optional

Alignment score.

Examples

>>> seq1 = NucleotideSequence("CGTCAT")
>>> seq2 = NucleotideSequence("TCATGC")
>>> matrix = SubstitutionMatrix.std_nucleotide_matrix()
>>> ali = align_optimal(seq1, seq2, matrix)[0]
>>> print(ali)
CGTCAT--
--TCATGC
>>> print(ali.trace)
[[ 0 -1]
 [ 1 -1]
 [ 2  0]
 [ 3  1]
 [ 4  2]
 [ 5  3]
 [-1  4]
 [-1  5]]
>>> print(ali[1:4].trace)
[[ 1 -1]
 [ 2  0]
 [ 3  1]]
>>> print(ali[1:4, 0:1].trace)
[[1]
 [2]
 [3]]
Attributes:
sequenceslist

A list of aligned sequences.

tracendarray, dtype=int, shape=(n,m)

The alignment trace.

scoreint

Alignment score.

get_gapped_sequences()

Get a the string representation of the gapped sequences.

Returns:
sequenceslist of str

The list of gapped sequence strings. The order is the same as in Alignment.sequences.

static trace_from_strings(seq_str_list)

Create a trace from strings that represent aligned sequences.

Parameters:
seq_str_listlist of str

The strings, where each each one represents a sequence (with gaps) in an alignment. A - is interpreted as gap.

Returns:
tracendarray, dtype=int, shape=(n,2)

The created trace.