`get_sequences`#

biotite.sequence.io.fasta.get_sequences(fasta_file, seq_type=None)[source]#

Get dictionary from a FastaFile instance, where headers are keys and sequences are values.

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.
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:

seq_dictdict: A dictionary that maps headers to NucleotideSequence and/or ProteinSequence instances as values.

Raises:

ValueError: If at least on of the sequence strings can be neither converted into a NucleotideSequence nor a ProteinSequence.

Gallery#

Customized visualization of a multiple sequence alignment

Customized visualization of a multiple sequence alignment