Nothing
test.isAdapter3.primeEnd <- function() {
adapter_seq <- "AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCG"
## Melanie's handcrafted example
highqualAdapterContamIn3PrimeEnd <-
"AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCG"
reads <- c( highqualAdapterContamIn3PrimeEnd )
observed = isAdapter(reads, 17, adapter_seqs = adapter_seq)
checkTrue(observed[1],
"isAdapter() does detect adapter in handcrafted example")
}
test.isAdapter <- function() {
adapter_seq <- "AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG"
l <- nchar(adapter_seq)
random_dna <- paste(sample(DNA_ALPHABET[1:4],
100, replace = TRUE),
collapse = '')
reads <- c(random_dna,
adapter_seq,
#read with full adapater and random
paste( c( adapter_seq, random_dna),
collapse = '' ),
#read with first part of adapter and random
paste(c(substr(adapter_seq, 1, 10), random_dna),
collapse = '' ),
#read with last part of adapter and random
paste(c(substr(adapter_seq, l - 10, l), random_dna),
collapse = '' )
)
# simply take 17 as threshold as this seemed to be one of the largest
# one we ever got from simulations
observed = isAdapter(reads, 17, adapter_seqs = adapter_seq)
checkTrue(!observed[1],
"isAdapter() does not flag random string as Adapter")
checkTrue(observed[2],
"isAdapter() does detect adapter")
checkTrue(observed[3],
"isAdapter() does detect adapter in longer read")
# Note that this guy is not flagged as adapter contam, and this is
# indeed what we want here
checkTrue(!observed[4],
"isAdapter() does not flag truncated adapter in longer read")
checkTrue(observed[5],
"isAdapter() does detect truncated adapter in longer read")
}
test.getAdapterSeqs <- function() {
adapter <- HTSeqGenie:::getAdapterSeqs(TRUE, TRUE, 1)
checkEquals(adapter, "AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCG",
"getAdapterSeqs() returns wrong adapter (Test1)" )
adapter <- HTSeqGenie:::getAdapterSeqs(TRUE, TRUE, 2)
checkEquals(adapter, "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT",
"getAdapterSeqs() returns wrong adapter (Test2)" )
adapter <- HTSeqGenie:::getAdapterSeqs(FALSE, FALSE, 1)
checkEquals(adapter, "AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG",
"getAdapterSeqs() returns wrong adapter (Test3)" )
adapter <- HTSeqGenie:::getAdapterSeqs(FALSE, TRUE, 1)
checkEquals(adapter, "AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCG",
"getAdapterSeqs() returns wrong adapter (Test4)" )
checkEquals(HTSeqGenie:::getAdapterSeqs(TRUE, TRUE , 1),
HTSeqGenie:::getAdapterSeqs(TRUE, FALSE, 1),
"getAdapterSeqs() should ignore forced_paired_end when paired_ends==TRUE")
}
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