# NOT RUN {
# get all available kingdoms for refseq
getKingdoms(db = "refseq")
# download all vertebrate genomes from refseq
meta.retrieval(kingdom = "vertebrate_mammalian",
db = "refseq",
type = "genome")
# get all available kingdoms for genbank
getKingdoms(db = "genbank")
# download all vertebrate genomes from genbank
meta.retrieval(kingdom = "vertebrate_mammalian",
db = "genbank",
type = "genome")
# get all available kingdoms for ensemblgenomes
getKingdoms(db = "ensemblgenomes")
# download all vertebrate genomes from ensemblgenomes
meta.retrieval(kingdom = "vertebrate_mammalian",
db = "ensemblgenomes",
type = "genome")
# In case users do not wish to retrieve genomes from an entire kingdom,
# but rather from a subgoup (e.g. from species belonging to the
# Gammaproteobacteria class, a subgroup of the bacteria kingdom),
# they can use the following workflow"
# First, users can again consult the getKingdoms() function to retrieve
# kingdom information.
getKingdoms(db = "refseq")
# In this example, we will choose the bacteria kingdom.
# Now, the getGroups() function allows users to obtain available
# subgroups of the bacteria kingdom.
getGroups(db = "refseq", kingdom = "bacteria")
# Now we choose the group Gammaproteobacteria and specify
# the group argument in the meta.retrieval() function
meta.retrieval(kingdom = "bacteria",
roup = "Gammaproteobacteria",
db = "refseq",
type = "genome")
# }
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