In ddiez/hmmertools: Run HMMER from R using Docker

library(BiocStyle)
library(hmmertools)

Introduction

hmmertools enables to run hmmer from R using a docker image.

h <- hmmertools::hmmer$new()
h

You can access methods help using help = TRUE or passing args = "-h" to HMMER methods.

#h$hmmsearch(help = TRUE)

You can specify the output file. By default hmmsearch outputs tbl format.

#seq <- system.file("files", "uniprot.fasta", package = "hmmertools")
#hmm <- system.file("files", "Ras.hmm", package = "hmmertools")
seq <- "uniprot.fasta"
hmm <- "Ras.hmm"
h$hmmsearch(hmmfile = hmm, seqdb = seq, outfile = "out.txt")
read.table("out.txt")

Align a set of sequences using a HMM profile:

h$hmmalign(hmmfile = hmm, seqfile = seq, outfile = "align.txt")
scan("align.txt", what = "", sep = "\n")

Build a HMM profile from an alignment.

h$hmmbuild(hmmfile = "hmm.txt", msafile = "align.txt")
scan("hmm.txt", what = "", sep = "\n")

Index a database of HMM profiles.

h$hmmpress(hmmfile = "hmm.txt")

Scan a set of sequences for hits from an (indexed) HMM profile database.

h$hmmscan(hmmdb = "hmm.txt", seqfile = seq, outfile = "scan.txt")
scan("scan.txt", what = "", sep = "\n")

ddiez/hmmertools documentation built on May 15, 2019, 1:51 a.m.