biotite.sequence.io.fasta.get_sequence

biotite.sequence.io.fasta.get_sequence(fasta_file, header=None)[source]

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.

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.