Multiple Sequence Alignment¶

Alignments¶

Alignment¶

class pytrimal.Alignment¶

A multiple sequence alignment.

__init__(names, sequences)¶

Create a new alignment with the given names and sequences.

Parameters

names (Sequence of bytes) – The names of the sequences in the alignment.
sequences (Sequence of str) – The actual sequences in the alignment.

Examples

Create a new alignment with a list of sequences and a list of names:

>>> alignment = Alignment(
...     names=[b"Sp8", b"Sp10", b"Sp26"],
...     sequences=[
...         "-----GLGKVIV-YGIVLGTKSDQFSNWVVWLFPWNGLQIHMMGII",
...         "-------DPAVL-FVIMLGTIT-KFS--SEWFFAWLGLEINMMVII",
...         "AAAAAAAAALLTYLGLFLGTDYENFA--AAAANAWLGLEINMMAQI",
...     ]
... )

There should be as many sequences as there are names, otherwise a ValueError will be raised:

>>> Alignment(
...     names=[b"Sp8", b"Sp10", b"Sp26"],
...     sequences=["GLQIHMMGII", "GLEINMMVII"]
... )
Traceback (most recent call last):
...
ValueError: `Alignment` given 3 names but 2 sequences

Sequence characters will be checked, and an error will be raised if they are not one of the characters from a biological alphabet:

>>> Alignment(
...     names=[b"Sp8", b"Sp10"],
...     sequences=["GLQIHMMGII", "GLEINMM123"]
... )
Traceback (most recent call last):
...
ValueError: The sequence "Sp10" has an unknown (49) character

copy()¶: Create a copy of this alignment.

load(path)¶

Load a multiple sequence alignment from a file.

Parameters: path (str, bytes or os.PathLike) – The path to the file containing the serialized alignment to load.
Returns: Alignment – The deserialized alignment.

Example

>>> msa = Alignment.load("example.001.AA.clw")
>>> msa.names
[b'Sp8', b'Sp10', b'Sp26', b'Sp6', b'Sp17', b'Sp33']

names¶

The names of the sequences in the alignment.

Type: sequence of bytes

residues¶

The residues in the alignment.

Type: AlignmentResidues

sequences¶

The sequences in the alignment.

Type: AlignmentSequences

Trimmed Alignment¶

class pytrimal.TrimmedAlignment(Alignment)¶

A multiple sequence alignment that has been trimmed.

Internally, the trimming process only produces a mask of sequences and a mask of residues. This class exposes the filtered sequences and residues.

__init__(names, sequences, sequences_mask=None, residues_mask=None)¶

Create a new alignment with the given names, sequences and masks.

Parameters

names (Sequence of bytes) – The names of the sequences in the alignment.
sequences (Sequence of str) – The actual sequences in the alignment.
sequences_mask (Sequence of bool) – A mask for which sequences to keep in the trimmed alignment. If given, must be as long as the sequences and names list.
residues_mask (Sequence of bool) – A mask for which residues to keep in the trimmed alignment. If given, must be as long as every element in the sequences argument.

names¶

The names of the sequences in the alignment.

Type: sequence of bytes

sequences¶

The sequences in the alignment.

Type: AlignmentSequences

Attributes¶

AlignmentSequences¶

class pytrimal.AlignmentSequences¶

A read-only view over the sequences of an alignment.

Objects from this class are created in the sequences property of Alignment objects. Use it to access the string data of individual rows from the alignment:

>>> msa = Alignment.load("example.001.AA.clw")
>>> len(msa.sequences)
6
>>> msa.sequences[0]
'-----GLGKVIV-YGIVLGTKSDQFSNWVVWLFPWNGLQIHMMGII'
>>> sum(letter == '-' for seq in msa.sequences for letter in seq)
43

AlignmentResidues¶

class pytrimal.AlignmentResidues¶

A read-only view over the residues of an alignment.

Objects from this class are created in the residues property of Alignment objects. Use it to access the string data of individual columns from the alignment:

>>> msa = Alignment.load("example.001.AA.clw")
>>> len(msa.residues)
46
>>> msa.residues[0]
'--A---'
>>> msa.residues[-1]
'IIIIFL'