@T.timeit<EOL><INDENT>def nt_db_search(self, files, base, unpack, euk_check,<EOL>search_method, maximum_range, threads, evalue):<DEDENT>
<EOL>hmmsearch_output_table = files.hmmsearch_output_path(base)<EOL>hit_reads_fasta = files.fa_output_path(base)<EOL>returnself.search_and_extract_nucleotides_matching_nucleotide_database(unpack,<EOL>euk_check,<EOL>search_method,<EOL>maximum_range,<EOL>threads,<EOL>evalue,<EOL>hmmsearch_output_table,<EOL>hit_reads_fasta)<EOL>
Nucleotide database search pipeline - pipeline where reads are searched
as nucleotides, and hits are identified using nhmmer searches

Parameters
----------
files : obj
    graftm_output_paths object.
base : str
    The name of the input file, stripped of all suffixes, and paths.
    Used for creating file names with 'files' object.
unpack : obj
    UnpackRawReads object, returns string command that will output
    sequences to stdout when called on command line
    (use: unpack.command_line())
euk_check : bool
    True indicates the sample will be checked for eukaryotic reads,
    False indicates not.
search_method : str
    The method for searching e.g. 'hmmsearch' or 'diamond'
maximum_range : int
    Maximum range that a gene can extend within a contig. Any hits
    that extend beyond this length cannot be linked. max_range is defined
    as 1.5 X the average length of all full length genes used in the
    search database. This is defined in the CONTENTS.json file within a
    gpkg.
threads : str
    Number of threads for hmmer to use
evalue : str
    Evalue cutoff for hmmer to use
Returns
-------
String path to amino acid fasta file of reads that hit