Downloads GFF3 and genomic FASTA with an optional VEuPathDB API key, or reads either input from a local file. Temporary downloads are deleted on exit. Returns a TxDb object, not an installable TxDb package.
Usage
easyTxDbmaker(
gff = NULL,
fasta = NULL,
abbr = "Pfalciparum3D7",
org = "Plasmodium falciparum",
taxid = 36329L,
db = "PlasmoDB release 71",
api_key = Sys.getenv("VEUPATHDB_API_KEY"),
timeout = 300,
verbose = TRUE
)Arguments
- gff
Local GFF3/GFF3.gz path or HTTPS URL.
- fasta
Optional local genomic FASTA/FASTA.gz path or HTTPS URL. Do not supply an AnnotatedTranscripts FASTA as chromosome information.
- abbr
Genome assembly label stored in the TxDb.
- org
Scientific organism name.
- taxid
NCBI taxonomy identifier.
- db
Description of the annotation source/release.
- api_key
Optional VEuPathDB bearer token; defaults to the VEUPATHDB_API_KEY environment variable. Sent only to trusted VEuPathDB- family hosts over HTTPS. Public URLs work without a key.
- timeout
Positive download timeout in seconds.
- verbose
Print status messages.
Details
IMPORTANT: fasta must contain genomic chromosome/contig sequences, NOT
annotated transcript sequences. If fasta = NULL, chromosome lengths are
not supplied explicitly; the GFF may still contain sequence metadata.
Examples
if (FALSE) { # \dontrun{
txdb <- easyTxDbmaker(gff = "https://plasmodb.org/a/service/raw-files/release-71/Pfalciparum3D7/gff/data/PlasmoDB-71_Pfalciparum3D7.gff", fasta = "https://plasmodb.org/a/service/raw-files/release-71/Pfalciparum3D7/fasta/data/PlasmoDB-71_Pfalciparum3D7_Genome.fasta")
# GFF-only, without explicit chromosome lengths:
txdb <- easyTxDbmaker(gff = "Pfalciparum3D7.gff", fasta = NULL)
# Offline use with accurate chromosome lengths:
txdb <- easyTxDbmaker(
gff = "Pfalciparum3D7.gff.gz",
fasta = "Pfalciparum3D7_Genome.fasta.gz"
)
} # }