`MSAInput`#

class biotite.application_v2.MSAInput(seqtype: Literal['nucleotide', 'protein'], sequences: list[Sequence], matrix: SubstitutionMatrix | None, original_sequences: list[Sequence])[source]#

Bases: object

The sequences and substitution matrix prepared for an MSA run.

Attributes:

seqtype{‘nucleotide’, ‘protein’}: The sequence type the software is run with. A mapped custom sequence type masquerades as 'protein'.
sequenceslist of Sequence: The sequences that are actually written to the input file. These may be mapped protein sequences.
matrixSubstitutionMatrix or None: The substitution matrix that is actually written to the input file, or None if no matrix is used.
original_sequenceslist of Sequence: The original input sequences, used to build the resulting Alignment.

static from_input(sequences: Sequence[Sequence], matrix: SubstitutionMatrix | None, supports_nucleotide: bool, supports_protein: bool, supports_custom_nucleotide_matrix: bool, supports_custom_protein_matrix: bool) → MSAInput#

Validate the input and determine how the sequences and substitution matrix are passed to the MSA software.

Sequences with an exotic alphabet are mapped onto protein sequences, if the software supports protein sequences with a custom substitution matrix.

Parameters:

sequencesiterable object of Sequence: The sequences to be aligned.
matrixSubstitutionMatrix or None: A custom substitution matrix.
supports_nucleotide, supports_proteinbool: Whether the software supports nucleotide or protein sequences, respectively.
supports_custom_nucleotide_matrix, supports_custom_protein_matrixbool: Whether the software supports custom substitution matrices for nucleotide or protein sequences, respectively.

Returns:

inputMSAInput: The prepared input.

read_fasta(file: IO[str]) → tuple[Alignment, ndarray]#

Read an MSA software’s FASTA output into an Alignment.

Parameters:

filefile object: The FASTA file written by the MSA software. The sequences must be identified by their input index.

Returns:

alignmentAlignment: The multiple sequence alignment.
orderndarray, dtype=int: The order of the sequences as intended by the MSA software.

write_fasta(file: IO[str]) → None#

Write the input sequences to a FASTA file, using their index as identifier.

Parameters:

filefile object: The file the sequences are written to.