Format fasta headers

Source: R/blast_result_parser.R

format the sequence headers for fasta file obtained from NCBI blast output

format_fasta_headers(fasta_file = NULL, keep_alignemnt_coord = TRUE)

Arguments

fasta_file

string denoting full path of a fasta file.
keep_alignemnt_coord

logical (default : TRUE) decides whether alignment coordinates to keep in headers or not. When TRUE header must contains alignment coordinates in this format :([:digit:]+-[:digit:]+). (e.g. CEJ90625.1:1-252)

Value

sequences as an object of class Biostrings

Examples

if (FALSE) {
 f <- system.file("extdata","blast_output_01.fasta" ,package = "phyloR")
 ## existing headers
 Biostrings::readAAStringSet(f) %>% names() %>% head()
 ## new  headers
 f %>% format_fasta_headers() %>% names() %>% head()
}