tests/test_seqTools.r

In seqTools: Analysis of nucleotide, sequence and quality content on fastq files

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## Load prerequisites
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library(seqTools)

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## Initialize example data
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basedir<-system.file("extdata",package="seqTools")

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## Run tests
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filename <- "test_seqTools.R"
basedir <- system.file("extdata", package = "seqTools")
load(file.path(basedir,"test_res.RData"))


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## countDnaKmers
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if(!identical(countDnaKmers("ACGT", k = 1, start = 3:1, width = 1), cdk_ACGT))
    stop("[countDnaKmers] Test 1 '", filename, "' FAILED!")

if(!identical(countDnaKmers("ACGT", k = 1, start = 3, width = 1), cdk_ACGT_one))
    stop("[countDnaKmers] Test 2 '", filename, "' FAILED!")

if(!identical(
        countDnaKmers("ATTNAC", k = 2, start = 1:3, width = 1), cdk_ATTNAC))
    stop("[countDnaKmers] Test 3 '", filename, "' FAILED!")

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## revCountDnaKmers
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if(!identical(
        revCountDnaKmers("ACGTACGT", k = 2, start = 6:4, width = 2), rck_ACGT))
    stop("[revCountDnaKmers] Test 1 '", filename, "' FAILED!")



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## END OF FILE
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