tests/test_read.R

In fishsciences/metabarcode_utils: Meta-barcoding Utilities

library(metabarcodeUtils)

f = system.file(package = "metabarcodeUtils",
                "sample_files",
                "BTWIT1-20200429B.xlsx")

out_dir = tempdir()

tt = mitofish_to_csv(f, outdir = out_dir)

ff = list.files(out_dir)

stopifnot(length(ff) == 2)
stopifnot(length(tt) == 2)

# test to fasta

csv_to_fasta(file.path(out_dir, ff[1]), outdir = out_dir)
ff = list.files(out_dir)
stopifnot(length(ff) == 3)

# test blank sheets
f = system.file(package = "metabarcodeUtils",
                "sample_files",
                "20210429TWI2A_A.xlsx")
tt = mitofish_to_csv(f, outdir = out_dir)

stopifnot(length(tt) == 2)
ff = list.files(out_dir)

csv_to_fasta(file.path(out_dir, "20210429TWI2A_A_hits.csv"), outdir = out_dir)

# Test nohits on hits tab
f = system.file(package = "metabarcodeUtils",
                "sample_files",
                "20210527TWI7A_B.xlsx")
tt = mitofish_to_csv(f, outdir = out_dir)