Retrieve sequences from genbank based on a dataset of accession numbers

Downloads sequences from genbank (nucleotide database) for particular taxa and genes into a folder called "0.Sequences".

Usage

sq.retrieve.indirect(acc.table, download.sqs = FALSE)

Arguments

acc.table: An accession table, ideally generated using acc.table.retrieve. The data.frame must have the Species, Acc, and gene column names.
download.sqs: Logical indicating whether sequences should be downloaded locally or returned as a list.

Value

None

Examples

if (FALSE) {
acc.table.retrieve(
 clades  = c('Felis', 'Vulpes', 'Phoca'),
 species = 'Manis_pentadactyla' ,
 genes   = c("A2AB","ADORA3","ADRB2","APOB",
            "APP","ATP7","BCHE","BDNF",
            "BMI1","BRCA1","BRCA2","CNR1",
            "COI","CREM","CYTB","DMP1",
            "EDG1","ENAM","FBN1","GHR",
            "IRBP","ND1","ND2","PLCB4",
            "PNOC","RAG1a","RAG1b","RAG2",
            "TTN","TYR1","VWF"),
 speciesLevel=TRUE
)

sq.retrieve.indirect(test)

}