biotite.sequence.io.fasta.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.