mmexport: Export DNA sequences of selected scaffolds

In KasperSkytte/mmgenome2: Tools for extracting individual genomes from metagenomes

Description

Writes the DNA sequences of a given set of scaffolds from the assembly to a FASTA file.

Usage

mmexport(
  scaffolds,
  assembly = get("assembly", envir = .GlobalEnv),
  file = "exported_assembly.fa"
)

Arguments

scaffolds	(required) Either a vector of scaffold names or a dataframe loaded with mmload containing the scaffolds to extract from the assembly.
assembly	(required) The assembly to subset and export. Must be an object of class "DNAStringSet" as loaded with readDNAStringSet. By default any object named "assembly" in the global environment will be used.
file	The file path and file name of the file to write the sequences to. (Default: "exported_assembly.fa")

Author(s)

Kasper Skytte Andersen [e-mail]

Soren M. Karst [e-mail]

Mads Albertsen [e-mail]

Examples

library(mmgenome2)
data(mmgenome2)
mmgenome2
selection <- data.frame(
  cov_C13.11.25 = c(7.2, 16.2, 25.2, 23.3, 10.1),
  cov_C14.01.09 = c(47, 77, 52.8, 29.5, 22.1)
)
mmgenome2_extraction <- mmextract(mmgenome2,
  min_length = 3000,
  selection = selection,
  inverse = FALSE
)
mmgenome2_extraction
## Not run: 
mmexport(mmgenome2_extraction,
  assembly = assembly,
  file = "bins/exported_assembly.fa"
)

## End(Not run)

KasperSkytte/mmgenome2 documentation built on Dec. 14, 2021, 12:11 a.m.