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Make a FASTA using UniProt accessions

make_fasta.Rd

Given a vector of UniProt accessions, this function will:

  1. Download the sequences

  2. Print the current UniProt release (you should put this in the FASTA file name)

  3. (Optional) add cRAP numbers to the FASTA headers for each sequence

  4. Save the sequences in a FASTA file

Usage

make_fasta(
  accessions,
  file,
  is_crap = FALSE,
  overwrite = FALSE,
  verbose = TRUE
)

Arguments

accessions

character vector, the UniProt accessions to use

file

character, filepath to save the fasta to e.g. "crap.fasta"

is_crap

logical, Is the output going to be a cRAP database? If TRUE cRAP001, cRAP002, etc. is appended to the sequence headers in the FASTA file. Default is FALSE

overwrite

logical, if the FASTA file already exists should it be overwritten? Default is FALSE

verbose

logical, should the function send messages to the console? Default is TRUE

Value

Returns a FASTA file saved to disk at the specified file path.

Examples

# specify some UniProt accessions
crap <- get_ccp_crap()
#> Error in get_ccp_crap(): could not find function "get_ccp_crap"

if (FALSE) { # \dontrun{
make_fasta(crap, "2021-01_cRAP.fasta")
} # }