make_fasta: Make a FASTA using UniProt accessions

In CambridgeCentreForProteomics/camprotR: Processing, analysing and visualising CCP proteomics data

Make a FASTA using UniProt accessions

Description

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()

## Not run: 
make_fasta(crap, "2021-01_cRAP.fasta")

## End(Not run)

CambridgeCentreForProteomics/camprotR documentation built on Jan. 27, 2023, 8:36 p.m.