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.