def hmmsearch(self, output_path, input_path, unpack, seq_type, threads, cutoff, orfm):
<EOL>logging.debug("<STR_LIT>" % (len(self.search_hmm)))<EOL>output_table_list = []<EOL>if len(self.search_hmm) > <NUM_LIT:1>:<EOL><INDENT>for hmm in self.search_hmm:<EOL><INDENT>out = os.path.join(os.path.split(output_path)[<NUM_LIT:0>], os.path.basename(hmm).split('<STR_LIT:.>')[<NUM_LIT:0>] + '<STR_LIT:_>' + os.path.split(output_path)[<NUM_LIT:1>])<EOL>output_table_list.append(out)<EOL><DEDENT><DEDENT>elif len(self.search_hmm) == <NUM_LIT:1>:<EOL><INDENT>output_table_list.append(output_path)<EOL><DEDENT>else:<EOL><INDENT>raise Exception("<STR_LIT>")<EOL><DEDENT>if seq_type == '<STR_LIT>':  <EOL><INDENT>input_cmd = orfm.command_line(input_path)<EOL><DEDENT>elif seq_type == '<STR_LIT>':  <EOL><INDENT>input_cmd = unpack.command_line()<EOL><DEDENT>else:<EOL><INDENT>raise Exception('<STR_LIT>')<EOL><DEDENT>if cutoff == "<STR_LIT>":<EOL><INDENT>searcher = HmmSearcher(threads, cutoff) <EOL><DEDENT>else:<EOL><INDENT>searcher = HmmSearcher(threads, '<STR_LIT>' % cutoff)<EOL><DEDENT>searcher.hmmsearch(input_cmd, self.search_hmm, output_table_list)<EOL>hmmtables = [HMMSearchResult.import_from_hmmsearch_table(x) for x in output_table_list]<EOL>return hmmtables<EOL>
hmmsearch - Search raw reads for hits using search_hmm list

Parameters
----------
output_path : str
    path to output domtblout table
input_path : str
    path to input sequences to search
unpack : UnpackRawReads
    UnpackRawReads object, returns string command that will output
    sequences to stdout when called on command line
    (use: unpack.command_line())
seq_type : str
    variable containing a string, either 'nucleotide' or 'aminoacid'.
    Tells the pipeline whether or not to call ORFs on the sequence.
    If sequence is 'nucleotide', ORFs are called. If not, no ORFs.
threads : Integer
    Number of threads to use. Passed to HMMsearch command.
cutoff : str
    cutoff for HMMsearch to use, either an evalue or --cut_tc, meaning
    use the TC score cutoff specified within the HMM. Passed to 
    HMMsearch command.
orfm : OrfM
    Object that builds the command chunk for calling ORFs on sequences
    coming through as stdin. Outputs to stdout. Calls command_line
    to construct final command line string.

Returns
-------
output_table_list : array of HMMSearchResult
    Includes the name of the output domtblout table given by hmmer

Raises
------
hmmsearcher.NoInputSequencesException
    Raised if there are no sequences fed into the HMM.