sequences_ex <- c(
"TACCTATGTTGCCTTGGCGGCTAAACCTACCCGGGATTTGATGGGGCGAATTACCTGGTATTTTAGCCCACTTACCCGGTACCAACCTACCCTGTACACCGCGCCTGGGTCTACCCTCCGGATGACATTTTTAAGACTCTTGTTTTATAGTGAAATTCTGAGTTTTTATACTTAATAAGTTAAAACTTTCAATCTCGGATCTCTTGGCTCTGGCATCGATGAAGAACGCTACGAAATGCTGATAAATAATGTGAATTGCCGAATTCATTGAATCATCGAATCTTTGAACGCACATTGCACCCATTAGTATTCTAGAGTGCATGCCTGTTCCAGCGTCATTTTCAATCCTCAAGCCCCTTATTGCTTGGTGTTGGCAGTTTAGCTGGCTTTATAGTGCTTAACTCCCTAAATATACTGCCTGATTCGCGGTGACCCCAAGCGTAATAATTATTTTCTCGCTTGAGGTG",
"TACCTATGTTGCCTTGGCGGCTAAACCTACCCGGGATTTGATGGGGCGAATTACCTGGTAAGGCCCACTTACCCGGTACCAACCTACCCTGTACACCGCGCCTGGGTCTACCCTCCGGATGACATTTTTAAGACTCTTGTTTTATAGTGAAATTCTGAGTTTTTATACTTAATAAGTTAAAACTTTCAATCTCGGATCTCTTGGCTCTGGCATCGATGAAGAACGCTACGAAATGCTGATAAATAATGTGAATTGCCGAATTCATTGAATCATCGAATCTTTGAACGCACATTGCACCCATTAGTATTCTAGAGTGCATGCCTGTTCCAGCGTCATTTTCAATCCTCAAGCCCCTTATTGCTTGGTGTTGGCAGTTTAGCTGGCTTTATAGTGCTTAACTCCCTAAATATACTGCCTGATTCGCGGTGACCCCAAGCGTAATAATTATTTTCTCGCTTGAGGTG",
"TACCTATGTTGCCTTGGCGGCTAAACCTACCCGGGATTTGATGGCGAATTACCTGGTATTTTAGCCCACTTACCCGGTACCAACCTACCCTGTACACCGCGCCTGGGTCTACCCTCCGGATGACATTTTTAAGACTCTTGTTTTATAGTGAAATTCTGAGTTTTTATACTTAATAAGTTAAAACTTTCAATCTCGGATCTCTTGGCTCTGGCATCGATGAAGAACGCTACGAAATGCTGATAAATAATGTGAATTGCCGAATTCATTGAATCATCGAATCTTTGAACGCACATTGCACCCATTAGTATTCTAGAGTGCATGCCTGTTCCAGCGTCATTTTCAATCCTCAAGCCCCTTATTGCTTGGTGTTGGCAGTTTAGCTGGCTTTATAGTGCTTAACTCCCTAAATATACTGCCTGATTCGCGGTGACCCCAAGCGTAATAATTATTTTCTCGCTTGAGGTG"
)
data("data_fungi")
df_basidio <- subset_taxa(data_fungi, Phylum == "Basidiomycota")
df_basidio <-
subset_taxa_pq(df_basidio, colSums(df_basidio@otu_table) > 1000)
# path_db <- "inst/extdata/100_sp_UNITE_sh_general_release_dynamic.fasta"
if (!MiscMetabar:::is_vsearch_installed()) {
message(
"vs_search_global() and asv2otu(..., method=vsearch) can't be tested when vsearch is not installed"
)
} else {
test_that("asv2otu works fine with vsearch method", {
expect_s4_class(
d_vs <-
asv2otu(data_fungi_sp_known, method = "vsearch"),
"phyloseq"
)
expect_s4_class(
d_fast <- asv2otu(
data_fungi_sp_known,
method = "vsearch",
vsearch_cluster_method = "--cluster_fast"
),
"phyloseq"
)
expect_s3_class(
asv2otu(dna_seq = sequences_ex, method = "vsearch"),
"data.frame"
)
expect_true(sum(!d_fast@refseq == d_vs@refseq) > 0)
expect_equal(sum(dim(d_vs@otu_table) == dim(d_fast@otu_table)), 2)
})
test_that("vs_search_global works fine with vsearch method", {
expect_s3_class(
res <- vs_search_global(data_fungi,
path_to_fasta = "inst/extdata/ex_little.fasta"
),
"data.frame"
)
expect_equal(dim(res), c(1420, 10))
expect_s3_class(
res <-
vs_search_global(data_fungi, sequences_ex),
"data.frame"
)
expect_s3_class(
res <-
vs_search_global(data_fungi, Biostrings::DNAStringSet(sequences_ex)),
"data.frame"
)
})
test_that("chimera_detection_vs works fine", {
expect_type(
chimera_fungi <- chimera_detection_vs(
seq2search = data_fungi@refseq,
nb_seq = taxa_sums(data_fungi)
),
"list"
)
expect_s4_class(chimera_fungi$non_chimera, "AAStringSet")
expect_equal(length(chimera_fungi$non_chimera), 1051)
expect_equal(length(chimera_fungi$chimera), 242)
expect_equal(length(chimera_fungi$borderline), 127)
})
test_that("chimera_detection_vs works fine", {
expect_s4_class(
data_fungi_nochim <-
chimera_removal_vs(data_fungi),
"phyloseq"
)
expect_equal(ntaxa(data_fungi_nochim), 1178)
expect_s4_class(
data_fungi_nochim_16 <- chimera_removal_vs(data_fungi,
abskew = 16,
min_seq_length = 10
),
"phyloseq"
)
expect_equal(ntaxa(data_fungi_nochim_16), 1259)
expect_s4_class(
data_fungi_nochim2 <-
chimera_removal_vs(data_fungi, type = "Select_only_non_chim"),
"phyloseq"
)
expect_equal(ntaxa(data_fungi_nochim2), 1051)
expect_s4_class(
data_fungi_chimera <-
chimera_removal_vs(data_fungi, type = "Select_only_chim"),
"phyloseq"
)
expect_equal(ntaxa(data_fungi_chimera), 242)
})
test_that("vsearch_clustering works fine", {
expect_s4_class(d_vs1 <- vsearch_clustering(data_fungi), "phyloseq")
expect_equal(ntaxa(d_vs1), 701)
expect_s4_class(d_vs2 <- vsearch_clustering(data_fungi,
id = 0.98,
vsearch_cluster_method = "--cluster_size"
), "phyloseq")
expect_equal(ntaxa(d_vs2), 817)
expect_s4_class(d_vs3 <- vsearch_clustering(data_fungi,
id = 0.98,
vsearch_cluster_method = "--cluster_smallmem",
vsearch_args = "--strand both --usersort"
), "phyloseq")
expect_type(
seq_clustered <- vsearch_clustering(dna_seq = sequences_ex),
"list"
)
expect_equal(dim(seq_clustered), c(4, 10))
})
}
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