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## tests use TP53 genome as fake rRNA genome
## First exon of TP53
## TTCCATACCTTCCAATTTTTCAAGGGAAGCTAGAAATCTCGATGTTCATGTGACAGCTCTTTTCTTCTTTATTTTTCAAATATTACCTTATTAAGGTATATTTTGCATATTCATATAATTTGCAGTGTATAATAATTTTTTAAATAAATTTACCAAGTTCTGCAACCATCACCATAAATCGGTTCATCAA
## RC: TTGATGAACCGATTTATGGTGATGGTTGCAGAACTTGGTAAATTTATTTAAAAAATTATTATACACTGCAAATTATATGAATATGCAAAATATACCTTAATAAGGTAATATTTGAAAAATAAAGAAGAAAAGAGCTGTCACATGAACATCGAGATTTCTAGCTTCCCTTGAAAAATTGGAAGGTATGGAA
test.detectRRNA <- function() {
## setup test framework
setupTestFramework(config.filename="test-data/test_config_single_end.txt", testname="test.detectRRNA",
config.update=list(
detectRRNA.rrna_genome = genome( TP53Genome()),
detectRRNA.do=TRUE) )
shortread1 <- ShortReadQ( DNAStringSet("TTCCATACCTTCCAATTTTTCAAGGGAAGCTAGAAATCTCGATGTTCATGT"),
quality = FastqQuality("bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb"),
id = BStringSet("tp53_substring_1_50#0/1"))
observed <- detectRRNA(list(shortread1, NULL) )
checkTrue(observed[1], "detectRRNA() detects rRNA in single end mode")
}
test.detectRRNA.paired_end <- function() {
## setup test framework
setupTestFramework(config.filename="test-data/test_config.txt",
testname="test.detectRRNA.paired_end",
config.update=list(
detectRRNA.do=TRUE,
detectRRNA.rrna_genome = genome( TP53Genome() )))
shortread1 <- ShortReadQ( DNAStringSet("TTCCATACCTTCCAATTTTTCAAGGGAAGCTAGAAATCTCGATGTTCATGT"),
quality = FastqQuality("bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb"),
id = BStringSet("tp53_substring_1_50#0/1"))
shortread2 <- ShortReadQ( DNAStringSet("GGCGCCCGCCTGCTCTCGGTGAGCGCACGTCCCGTGCTCCCCTCTGGCGGG"),
quality = FastqQuality("bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb"),
id = BStringSet("tp53_substring_1_50#0/2"))
observed <- detectRRNA(list(shortread1, shortread2))
checkTrue(observed[[1]], "detectRRNA() detects rRNA in paired end mode")
}
test.getRRNAIds <- function() {
## make test files
tmpdir <- HTSeqGenie:::createTmpDir(prefix="test_get_rRNA_ids")
file1 <- file.path(tmpdir, "1.fastq")
file2 <- file.path(tmpdir, "2.fastq")
shortread1 <- ShortReadQ( DNAStringSet("TTCCATACCTTCCAATTTTTCAAGGGAAGCTAGAAATCTCGATGTTCATGT"),
quality = FastqQuality("bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb"),
id = BStringSet("tp53_substring_1_50#0/1"))
shortread2 <- ShortReadQ( DNAStringSet("GGCGCCCGCCTGCTCTCGGTGAGCGCACGTCCCGTGCTCCCCTCTGGCGGG"),
quality = FastqQuality("bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb"),
id = BStringSet("tp53_substring_1_50#0/2"))
writeFastq(shortread1, file=file1, lane='', compress=FALSE)
writeFastq(shortread2, file=file2, lane='', compress=FALSE)
## run the function to test
ids <- getRRNAIds(file1 = file1,
file2 = file2,
tmp_dir = tmpdir,
rRNADb = genome( TP53Genome() ))
checkEquals(ids[1], "tp53_substring_1_50#0", "get_rRNA_ids() does detect rRNA seqs")
unlink(tmpdir, recursive=TRUE)
}
test.getRRNAIds_random <-function() {
## random seqs that should not match rRNA
tmpdir <- HTSeqGenie:::createTmpDir(prefix="test_get_rRNAIds_random")
file1 <-file.path(tmpdir, "1.fastq")
random_sreads <- HTSeqGenie:::makeRandomSreads(100,100)
writeFastq(random_sreads, file=file1, lane='', compress=FALSE)
ids <- getRRNAIds(file1 = file1,
tmp_dir = tmpdir,
rRNADb = genome( TP53Genome() ))
checkEquals(length(ids), 0, "get_rRNA_ids() does not find rRNAs in random strings")
unlink(tmpdir, recursive=TRUE)
}
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