run_hmmsearch: Run Hmmsearch

In djw533/micro.gen.extra: Microbial genomics extensions and functions

Run Hmmsearch

Description

Run hmmsearch and store tabular data frame, domain tabular output data frame, and an alignment of the domain hits in a list

Usage

run_hmmsearch(
  query,
  hmm_profile,
  input_format = c("fasta", "AAStringSet"),
  output_dir = "temp_hmmsearch",
  cutoff = 20,
  cpu = 1,
  clean = T
)

Arguments

query	fasta file or Biostrings AAStringSet
hmm_profile	Hmm profile file (with at least one profile hmm)
input_format	Query input format. One of ["fasta", "AAStringSet"],
output_dir	Output directory.
cutoff	Hmmer score cutoff. [Default = 20]
cpu	Number of threads to use. [Default = 1]
clean	Remove output directory and contents. [Default = TRUE]

Value

Whole sequence and per-domain hmmsearch results as dataframes, and alignment of hits as alignment in Biostrings format

djw533/micro.gen.extra documentation built on Nov. 8, 2024, 5:11 a.m.