inst/tinytest/test-read_fasta.R

In jedick/canprot: Chemical Analysis of Proteins

# Test added on 20230304
info <- "read_fasta() recognizes type, iseq, start, stop arguments"
# Read protein IDs, sequence start/stop positions, and midpoint potentials
data_file <- system.file("extdata/fasta/redoxin.csv", package = "canprot")
dat <- read.csv(data_file)
# Read header lines
fasta_file <- system.file("extdata/fasta/redoxin.fasta", package = "canprot")
headers <- read_fasta(fasta_file, type = "header")
# Locate the sequences in the FASTA file
iseqs <- sapply(dat$ID, grep, x = headers)
expect_equal(iseqs, c(5, 11, 6, 2, 8, 7, 1, 9, 10, 3, 4), check.names = FALSE, info = info)
# Loop over proteins
aalist <- lapply(1:nrow(dat), function(i) {
  # Read the amino acid composition of this protein
  read_fasta(fasta_file, iseq = iseqs[i], start = dat$start[i], stop = dat$stop[i])
})
aa <- do.call(rbind, aalist)
expect_equal(gsub(".*\\|", "", aa$protein), dat$ID, info = info)
expect_equal(plength(aa), dat$stop - dat$start + 1, info = info)
Zc_ref <- c(-0.223485, -0.09324, -0.126904, -0.139984, -0.166184,
  -0.159664, -0.048673, -0.235294, -0.05036, -0.22028, -0.265018)
expect_equal(round(Zc(aa), 6), Zc_ref, info = info)

# Test added on 20230308
info <- "read_fasta() handles 0-length 'iseq' argument"
fasta_file <- system.file("extdata/fasta/redoxin.fasta", package = "canprot")
expect_equal(nrow(read_fasta(fasta_file, iseq = numeric())), 0, info = info)

# Moved from CHNOSZ on 20240328
info <- "read_fasta() reads selected sequences correctly"
fasta_file <- system.file("extdata/fasta/redoxin.fasta", package = "canprot")
aa <- read_fasta(fasta_file)
aa1 <- read_fasta(fasta_file, 1)
expect_equal(aa1, aa[1, ], info = info)
aa8rev <- read_fasta(fasta_file, 8:1)
# Use unlist here so that different row names are not compared
expect_equal(unlist(aa8rev), unlist(aa[8:1, ]), info = info)