hmmSearch: Run hmmsearch (HMMER 3)

Description Usage Arguments Value

View source: R/internals.R

Description

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

Usage

1
hmmSearch(bin, fasta, hmm, oty = "domtblout", cut = "ga", n_threads = 1L)

Arguments

bin

The location of hmmsearch binary.

fasta

A protein fasta file.

hmm

A hmm file. Must be pressed (see hmmpress from HMMER manual).

oty

The hmmsearch output type.

cut

One of "ga" or "tc". See HMMER 3.1b2 manual.

n_threads

An integer. The number of cores to use.

Value

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


iferres/dcda documentation built on Nov. 19, 2017, 2:24 p.m.