get_alignment

biotite.sequence.io.fasta.get_alignment(fasta_file, additional_gap_chars=('_',), seq_type=None)

Get an alignment from a FastaFile instance.

Parameters:

fasta_fileFastaFile

The FastaFile to be accessed.

additional_gap_charsstr, optional

The characters to be treated as gaps.

seq_typeClass, optional

The Sequence subclass contained in the file. If not set, biotite will attempt to automatically detect whether a nucleotide or protein sequence is present.

Returns:

alignmentAlignment

The alignment from the FastaFile.