get_ref_name.Rscript

#!/usr/bin/env Rscript
options(error = quote({
	dump.frames(to.file=TRUE, dumpto="Rcoredump")
	load("Rcoredump.rda")
	print(Rcoredump)
	q()
}))
help = paste(
"get_ref_name.Rscript Read the name of the supplied reference genome",
"Daniel Wilson (2022)",
"",
"Usage: Rscript get_ref_name.Rscript fasta_file",
sep="\n")

# Read options from command line
args = commandArgs(trailingOnly = TRUE)
if(length(args)!=1) {
	cat(help,file=stderr(),sep="\n")
	stop("\nIncorrect usage\n")
}
REF_FA = args[1]

ref.name = scan(REF_FA, what=character(0), sep='\n', nlines=1, quiet=TRUE)
ref.name = unlist(strsplit(ref.name, ' '))[1]
if(substr(ref.name,1,1)!='>') {
	stop('Error: reference fasta file does not begin with a name starting with >','\n')
}
ref.name = substr(ref.name,2,1e6)
cat(ref.name,file=stdout())