augur.io.sequences

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.).

Parameters:
  • 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.).

Yields:

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.

Parameters:
  • records (iterable of dict) – Iterator that yields dict that contains sequences

  • fasta (str) – Path to FASTA file

  • seq_id_field (str, optional) – Field name for the sequence identifier

  • seq_field (str, optional) – Field name for the genomic sequence

Yields:

dict – A copy of the record with seq_field dropped

Raises:

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.

Parameters:
  • 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.)

Returns:

Number of sequences written out to the given path.

Return type:

int