get_sequence

biotite.sequence.io.fasta.get_sequence(fasta_file, header=None, seq_type=None)

Get a sequence from a FastaFile instance.

The type of sequence is guessed from the sequence string: First, a conversion into a NucleotideSequence and second a conversion into a ProteinSequence is tried.

Parameters:

fasta_fileFastaFile

The FastaFile to be accessed.

headerstr, optional

The header to get the sequence from. By default, the first sequence of the file is returned.

seq_typetype[Sequence], optional

The Sequence subclass contained in the file. If not set, the type is automatically inferred as ProteinSequence or NucleotideSequence. For large sequence data it is recommended to set this parameter.

Returns:

sequenceNucleotideSequence or ProteinSequence

The requested sequence in the FastaFile. NucleotideSequence if the sequence string fits the corresponding alphabet, ProteinSequence otherwise.

Raises:

ValueError

If the sequence data can be neither converted into a NucleotideSequence nor a ProteinSequence.

Gallery

Homology search and multiple sequence alignment

Homology search and multiple sequence alignment