def kmer_lca_records(seqs_path,
                     one_codex_api_key: 'One Codex API key' = None,
                     fastq: 'input is fastq; disable autodetection' = False,
                     progress: 'show progress bar (sent to stderr)' = False):
    '''
    Parallel lowest common ancestor sequence classification of fasta/q using the One Codex API.
    Returns Biopython SeqRecords with tictax annotations as the `description` attribute.
    LCAs are assigned using an LCA index of 31mers from the One Codex database.
    '''
    records = parse_seqs(seqs_path, fastq)
    one_codex_api_key = one_codex_api_key if one_codex_api_key else config()['one_codex_api_key']
    print('Classifying sequences…', file=sys.stderr)
    records = asyncio.get_event_loop().run_until_complete(oc_classify(records,
                                                                      one_codex_api_key,
                                                                      progress,
                                                                      False))
    return records
def kmer_lca_records ( seqs_path , one_codex_api_key : 'One Codex API key' = None , fastq : 'input is fastq; disable autodetection' = False , progress : 'show progress bar (sent to stderr)' = False ) : records = parse_seqs ( seqs_path , fastq ) one_codex_api_key = one_codex_api_key if one_codex_api_key else config ( ) [ 'one_codex_api_key' ] print ( 'Classifying sequences…' , file = sys . stderr ) records = asyncio . get_event_loop ( ) . run_until_complete ( oc_classify ( records , one_codex_api_key , progress , False ) ) return records
Parallel lowest common ancestor sequence classification of fasta/q using the One Codex API.
    Returns Biopython SeqRecords with tictax annotations as the `description` attribute.
    LCAs are assigned using an LCA index of 31mers from the One Codex database.