run.hmmsearch: Run hmmsearch (HMMER 3)

In ukaraoz/microtrait: microTrait

Run hmmsearch (HMMER 3)

Description

Takes a fasta file and a Hidden Markov Model profile and performs a search of the former over the latter.

Usage

run.hmmsearch(
  faa_file = system.file("extdata", "2619619645.genes.faa", package = "microtrait",
    mustWork = TRUE),
  hmm = NULL,
  domtblout_file = NULL,
  n_threads = 1
)

Arguments

hmm	A hmm file. Must be pressed (see hmmpress from HMMER manual).
domtblout_file
n_threads	An integer. The number of cores to use.
fasta	A protein fasta file.

Value

The path to a temporary file where the hmmsearch output is placed.

hmmsearch –cpu $ncpus –domtblout $faafile".microtrait.domtblout" $hmm $faafile > /dev/null

ukaraoz/microtrait documentation built on March 18, 2024, 5:47 p.m.