inst/extdata/ad_hoc_misc_testing.R

In adsteen/genomechop:

# Testign script

## INCORPORATE THESE AS UNIT TESTS

load_all()

# Test circular cut
test.str <- letters
circular_cut(seq = test.str, len = 5, start.pos = 1) # works
circular_cut(seq = test.str, len = 5, start.pos = 23) # returns letters


# Try running circular_chop with a vector of sequences
test.str <- c("actgaa", "agacct", "gatcac")
circular_cut(test.str, len=rep(3, 3), start.pos = c(1, 3, 6))


# Given a fasta filename:
fasta.fn <- "inst/extdata/GCF_000567945.1_ASM56794v1_genomic.fna"

example.fasta <- read.fasta(fasta.fn)
str(example.fasta)
# One sequence, I think
example.seq <- example.fasta[[1]]
#bunch.o.chops <- lapply(example.fasta, chop_fasta, len = 1000, "complete")