setHMM: Prepare Compressed Hmm Files To Hmmsearch

In iferres/phylen: Search Core Genes Using HMMs, Compute Multiple Alignment, Concatenate And Compute Phylogeny

Description

Decompress, concatenate and press (hmmpress) hmm files to allow hmmsearch to run.

Usage

setHmm(hmm = character(), isCompressed = TRUE)

Arguments

hmm	The path to the .hmm.tar.gz file downloaded from EggNOG website, or the already prepared hmm text file.
isCompressed	logical() If the hmm points to the hmm.tar.gz file, it should be set to TRUE. If the pipeline has been already ran, the hmm parameter should point to the ".hmm" file that was generated.

Details

If the pipeline was ran before, the function will also check for index files and will produce them if any of the required is missing. See "hmmpress" from HMMER 3.1b2 manual.

Value

A character vector with the names of the hmm file and their indices.

Author(s)

Ignacio Ferres

iferres/phylen documentation built on May 24, 2019, 2:04 a.m.