append_fasta: Append sequences to end of a FASTA

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

Append sequences to end of a FASTA

Description

This function is used to add sequences from a FASTA file (file1) onto the end of another FASTA file (file2).

If file2 is a cRAP database, then you can optionally add cRAP numbers to the headers of file1, starting at the desired number e.g. cRAP127.

Usage

append_fasta(file1, file2, is_crap = FALSE, crap_start = 1)

Arguments

file1	character, file path of FASTA to append
file2	character, file path of FASTA to append to
is_crap	logical, should cRAP numbers e.g. cRAP001, cRAP002, etc. be added to sequence headers of file1? Default is FALSE
crap_start	numeric, what number should the cRAP00x start at? Default is 1.

Value

Overwrites FASTA file2 with some more sequences added to the end.

Examples

# Add some commercial protease sequences onto the end of CCP cRAP FASTA
## Not run: 
append_fasta(
  file1 = "commercial-proteases.fasta",
  file2 = "2021-01_CCP_cRAP.fasta",
  is_crap = TRUE,
  crap_start = 128
)

## End(Not run)

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