load_genbank_annotations: Given a genbank accession, make a txDb object along with...

In elsayed-lab/hpgltools: A pile of (hopefully) useful R functions

Given a genbank accession, make a txDb object along with sequences, etc.

Description

Let us admit it, sometimes biomart is a pain. It also does not have easily accessible data for microbes. Genbank does!

Usage

load_genbank_annotations(
  accession = "AE009949",
  file = NULL,
  sequence = TRUE,
  reread = TRUE,
  savetxdb = FALSE
)

Arguments

accession	Accession to download and import.
file	Use a file instead of downloading the accession?
sequence	Download the sequence with the annotations?
reread	Re-read (download) the file from genbank.
savetxdb	Attempt saving a txdb object?

Details

Tested in test_40ann_biomartgenbank.R and test_70expt_spyogenes.R This primarily sets some defaults for the genbankr service in order to facilitate downloading genomes from genbank and dumping them into a local txdb instance.

Value

List containing a txDb, sequences, and some other stuff which I haven't yet finalized.

See Also

[Biostrings] [GenomicFeatures] [genbankr::import()] [genbankr::readGenBank()]

Examples

 sagalacticae_genbank_annot <- load_genbank_annotations(accession = "AE009948")
 dim(as.data.frame(sagalacticae_genbank_annot$cds))

elsayed-lab/hpgltools documentation built on May 9, 2024, 5:02 a.m.