- augur.io.sequences.read_sequences(*paths, format='fasta')
Read sequences from one or more paths.
Automatically infer compression mode (e.g., gzip, etc.) and return a stream of sequence records in the requested format (e.g., “fasta”, “genbank”, etc.).
paths (list of str or os.PathLike) – One or more paths to sequence files of any type supported by BioPython.
format (str) – Format of input sequences matching any of those supported by BioPython (e.g., “fasta”, “genbank”, etc.).
Bio.SeqRecord.SeqRecord – Sequence record from the given path(s).
- augur.io.sequences.write_records_to_fasta(records, fasta, seq_id_field='strain', seq_field='sequence')
Write sequences from dict records to a fasta file. Yields the records with the seq_field dropped so that they can be consumed downstream.
dict – A copy of the record with seq_field dropped
AugurError – When the sequence id field or sequence field does not exist in a record
- augur.io.sequences.write_sequences(sequences, path_or_buffer, format='fasta')
Write sequences to a given path in the given format.
Automatically infer compression mode (e.g., gzip, etc.) based on the path’s filename extension.
sequences (iterable of Bio.SeqRecord.SeqRecord) – A list-like collection of sequences to write
path_or_buffer (str or os.PathLike or io.StringIO) – A path to a file to write the given sequences in the given format.
format (str) – Format of input sequences matching any of those supported by BioPython (e.g., “fasta”, “genbank”, etc.)
Number of sequences written out to the given path.
- Return type: