Nothing
################################################################################
#' Search for a list of sequence in a fasta file against physeq reference
#' sequences using [vsearch](https://github.com/torognes/vsearch)
#'
#' `r lifecycle::badge("maturing")`
#'
#' @inheritParams clean_pq
#' @param seq2search (required if path_to_fasta is NULL) Either (i) a DNAstringSet object
#' or (ii) a character vector that will be convert to DNAstringSet using
#' [Biostrings::DNAStringSet()]
#' @param path_to_fasta (required if seq2search is NULL) a path to fasta file if seq2search is est to NULL.
#' @param vsearchpath (default: vsearch) path to vsearch
#' @param id (default: 0.8) id for the option `--usearch_global` of the vsearch software
#' @param iddef (default: 0) iddef for the option `--usearch_global` of the vsearch software
#' @param keep_temporary_files (logical, default: FALSE) Do we keep temporary files
#' - temp.fasta (refseq in fasta)
#' - cluster.fasta (centroid)
#' - temp.uc (clusters)
#' @examplesIf MiscMetabar::is_vsearch_installed()
#' \donttest{
#' if (requireNamespace("seqinr")) {
#' file_dna <- tempfile("dna.fa")
#' seqinr::write.fasta("GCCCATTAGTATTCTAGTGGGCATGCCTGTTCGAGCGTCATTTTCAACC",
#' file = file_dna, names = "seq1"
#' )
#'
#' res <- vs_search_global(data_fungi, path_to_fasta = file_dna)
#' unlink(file_dna)
#'
#' res[res$identity != "*", ]
#'
#' clean_pq(subset_taxa(data_fungi, res$identity != "*"))
#' }
#' }
#' @return A dataframe with uc results (invisible)
#' @export
#' @details
#' This function is mainly a wrapper of the work of others.
#' Please cite [vsearch](https://github.com/torognes/vsearch).
#' @author Adrien Taudière
vs_search_global <- function(physeq,
seq2search = NULL,
path_to_fasta = NULL,
vsearchpath = "vsearch",
id = 0.8,
iddef = 0,
keep_temporary_files = FALSE) {
verify_pq(physeq)
dna <- Biostrings::DNAStringSet(physeq@refseq)
Biostrings::writeXStringSet(dna, paste0(tempdir(), "/", "temp.fasta"))
if (is.null(seq2search) && is.null(path_to_fasta)) {
stop("You must fill either seq2search or path_to_fasta argument.")
}
if (!is.null(seq2search) && !is.null(path_to_fasta)) {
stop("You must set either seq2search or path_to_fasta but not both.")
}
if (!is.null(seq2search)) {
if (inherits(seq2search, "character")) {
seq2search <- Biostrings::DNAStringSet(seq2search)
}
Biostrings::writeXStringSet(seq2search, paste0(tempdir(), "seq2search.fasta"))
seq2search <- paste0(tempdir(), "seq2search.fasta")
} else if (!is.null(path_to_fasta)) {
dna <- Biostrings::readDNAStringSet(path_to_fasta)
Biostrings::writeXStringSet(dna, paste0(tempdir(), "seq2search.fasta"))
seq2search <- paste0(tempdir(), "seq2search.fasta")
}
system2(
vsearchpath,
paste(
" --usearch_global ",
paste0(tempdir(), "/", "temp.fasta"),
" --db ",
seq2search,
" --uc ",
paste0(tempdir(), "/", "temp.uc"),
" --id ",
id,
" --uc_allhits",
" --strand both",
" --iddef ",
iddef,
sep = ""
)
)
pack_clusts <-
utils::read.table(paste0(tempdir(), "/", "temp.uc"), sep = "\t")
colnames(pack_clusts) <- c(
"type",
"cluster",
"width",
"identity",
"strand",
"6",
"7",
"cigarAlignment",
"query",
"target"
)
if (!keep_temporary_files) {
if (file.exists(paste0(tempdir(), "temp.fasta"))) {
unlink(paste0(tempdir(), "temp.fasta"))
}
if (file.exists(paste0(tempdir(), "temp.uc"))) {
unlink(paste0(tempdir(), "temp.uc"))
}
if (file.exists(paste0(tempdir(), "seq2search.fasta"))) {
unlink(paste0(tempdir(), "seq2search.fasta"))
}
} else {
message(paste0("Temporary files are located at ", tempdir()))
}
return(invisible(pack_clusts))
}
################################################################################
###############################################################################
#' Re-cluster sequences of an object of class `physeq`
#' or cluster a list of DNA sequences using SWARM
#'
#' @description
#' `r lifecycle::badge("maturing")`
#'
#' @inheritParams clean_pq
#' @param dna_seq NOT WORKING FOR THE MOMENT
#' You may directly use a character vector of DNA sequences
#' in place of physeq args. When physeq is set, dna sequences take the value of
#' `physeq@refseq`
#' @param d (default: 1) maximum number of differences allowed between two
#' amplicons, meaning that two amplicons will be grouped if they have `d`
#' (or less) differences
#' @param swarmpath (default: swarm) path to swarm
#' @param vsearch_path (default: vsearch) path to vsearch, used only if physeq
#' is NULL and dna_seq is provided.
#' @param nproc (default: 1)
#' Set to number of cpus/processors to use for the clustering
#' @param swarm_args (default : "--fastidious") a one length character
#' element defining other parameters to passed on to swarm See other possible
#' methods in the [SWARM pdf manual](https://github.com/torognes/swarm/blob/master/man/swarm_manual.pdf)
#' @param tax_adjust (Default 0) See the man page
#' of [merge_taxa_vec()] for more details.
#' To conserved the taxonomic rank of the most abundant ASV,
#' @param keep_temporary_files (logical, default: FALSE) Do we keep temporary
#' files ?
#' - temp.fasta (refseq in fasta or dna_seq sequences)
#' - temp_output (classical output of SWARM)
#' - temp_uclust (clusters output of SWARM)
#' @details This function use the `merge_taxa_vec` function to
#' merge taxa into clusters. By default tax_adjust = 0. See the man page
#' of [merge_taxa_vec()].
#' @return A new object of class `physeq` or a list of cluster if dna_seq
#' args was used.
#'
#' @references
#' SWARM can be downloaded from
#' \url{https://github.com/torognes/swarm/}.
#'
#' @export
#' @examplesIf MiscMetabar::is_swarm_installed()
#' summary_plot_pq(data_fungi)
#' system2("swarm", "-h")
#'
#' data_fungi_swarm <- swarm_clustering(data_fungi)
#' summary_plot_pq(data_fungi_swarm)
#'
#' sequences_ex <- c(
#' "TACCTATGTTGCCTTGGCGGCTAAACCTACCCGGGATTTGATGGGGCGAATTAATAACGAATTCATTGAATCA",
#' "TACCTATGTTGCCTTGGCGGCTAAACCTACCCGGGATTTGATGGGGCGAATTACCTGGTAAGGCCCACTT",
#' "TACCTATGTTGCCTTGGCGGCTAAACCTACCCGGGATTTGATGGGGCGAATTACCTGGTAGAGGTG",
#' "TACCTATGTTGCCTTGGCGGCTAAACCTACC",
#' "CGGGATTTGATGGCGAATTACCTGGTATTTTAGCCCACTTACCCGGTACCATGAGGTG",
#' "GCGGCTAAACCTACCCGGGATTTGATGGCGAATTACCTGG",
#' "GCGGCTAAACCTACCCGGGATTTGATGGCGAATTACAAAG",
#' "GCGGCTAAACCTACCCGGGATTTGATGGCGAATTACAAAG",
#' "GCGGCTAAACCTACCCGGGATTTGATGGCGAATTACAAAG"
#' )
#'
#' sequences_ex_swarm <- swarm_clustering(
#' dna_seq = sequences_ex
#' )
#' @seealso [asv2otu()], [vsearch_clustering()]
#' @references
#' SWARM can be downloaded from
#' \url{https://github.com/torognes/swarm}.
#' More information in the associated publications
#' \doi{doi:10.1093/bioinformatics/btab493} and \doi{doi:10.7717/peerj.593}
#' @details
#' This function is mainly a wrapper of the work of others.
#' Please cite [SWARM](https://github.com/torognes/swarm).
swarm_clustering <- function(physeq = NULL,
dna_seq = NULL,
d = 1,
swarmpath = "swarm",
vsearch_path = "vsearch",
nproc = 1,
swarm_args = "--fastidious",
tax_adjust = 0,
keep_temporary_files = FALSE) {
dna <- physeq_or_string_to_dna(
physeq = physeq,
dna_seq = dna_seq
)
if (!is.null(physeq)) {
nseq <- taxa_sums(physeq)
nseq <- nseq[match(names(nseq), names(dna))]
names(dna) <- paste0(names(dna), "_", nseq)
Biostrings::writeXStringSet(dna, paste0(tempdir(), "/", "temp.fasta"))
system2(
swarmpath,
paste0(
paste0(tempdir(), "/", "temp.fasta"),
" -o ",
paste0(tempdir(), "/", "temp_output"),
" ",
" -u ",
paste0(tempdir(), "/", "temp_uclust"),
" -t ",
nproc,
" ",
swarm_args
),
stdout = TRUE,
stderr = TRUE
)
} else {
Biostrings::writeXStringSet(dna, paste0(tempdir(), "/", "amplicons.fasta"))
system2(
vsearch_path,
paste0(
" --derep_fulllength ",
paste0(tempdir(), "/", "amplicons.fasta"),
" --sizeout --relabel_sha1 --fasta_width 0 --output ",
paste0(tempdir(), "/", "temp.fasta")
),
stdout = TRUE,
stderr = TRUE
)
system2(
swarmpath,
paste0(
paste0(tempdir(), "/", "temp.fasta"),
" -o ",
paste0(tempdir(), "/", "temp_output"),
" ",
" -u ",
paste0(tempdir(), "/", "temp_uclust"),
" -z ",
" -t ",
nproc,
" ",
swarm_args
),
stdout = TRUE,
stderr = TRUE
)
}
pack_clusts <-
utils::read.table(paste0(tempdir(), "/", "temp_uclust"), sep = "\t")
colnames(pack_clusts) <-
c(
"type",
"cluster",
"width",
"identity",
"strand",
"6",
"7",
"cigarAlignment",
"query",
"target"
)
if (inherits(physeq, "phyloseq")) {
clusters <- pack_clusts$cluster[pack_clusts$type != "C"]
names(clusters) <-
sub("_.*$", "", pack_clusts$query[pack_clusts$type != "C"])
clusters <- clusters[match(taxa_names(physeq), names(clusters))]
new_obj <-
merge_taxa_vec(physeq,
clusters,
tax_adjust = tax_adjust
)
} else if (inherits(dna_seq, "character")) {
new_obj <- pack_clusts
} else {
stop(
"You must set the args physeq (object of class phyloseq) or
dna_seq (character vector)."
)
}
if (file.exists(paste0(tempdir(), "/", "temp.fasta")) &&
!keep_temporary_files) {
unlink(paste0(tempdir(), "/", "temp.fasta"))
}
if (file.exists(paste0(tempdir(), "/", "temp_output")) &&
!keep_temporary_files) {
unlink(paste0(tempdir(), "/", "temp_output"))
}
if (file.exists(paste0(tempdir(), "/", "temp_uclust")) &&
!keep_temporary_files) {
unlink(paste0(tempdir(), "/", "temp_uclust"))
}
if (file.exists(paste0(tempdir(), "/", "amplicon.fasta")) &&
!keep_temporary_files) {
unlink(paste0(tempdir(), "/", "amplicon.fasta"))
}
return(new_obj)
}
###############################################################################
###############################################################################
#' Recluster sequences of an object of class `physeq`
#' or cluster a list of DNA sequences using vsearch software
#'
#' @description
#' `r lifecycle::badge("maturing")`
#'
#' @inheritParams clean_pq
#' @param dna_seq You may directly use a character vector of DNA sequences
#' in place of physeq args. When physeq is set, dna sequences take the value of
#' `physeq@refseq`
#' @param nproc (default: 1)
#' Set to number of cpus/processors to use for the clustering
#' @param id (default: 0.97) level of identity to cluster
#' @param vsearchpath (default: vsearch) path to vsearch
#' @param tax_adjust (Default 0) See the man page
#' of [merge_taxa_vec()] for more details.
#' To conserved the taxonomic rank of the most abundant ASV,
#' set tax_adjust to 0 (default). For the moment only tax_adjust = 0 is
#' robust
#' @param vsearch_cluster_method (default: "--cluster_size) See other possible
#' methods in the [vsearch manual](https://github.com/torognes/vsearch) (e.g. `--cluster_size` or `--cluster_smallmem`)
#' - `--cluster_fast` : Clusterize the fasta sequences in filename, automatically sort by decreasing sequence length beforehand.
#' - `--cluster_size` : Clusterize the fasta sequences in filename, automatically sort by decreasing sequence abundance beforehand.
#' - `--cluster_smallmem` : Clusterize the fasta sequences in filename without automatically modifying their order beforehand. Sequence are expected to be sorted by decreasing sequence length, unless *--usersort* is used.
#' In that case you may set `vsearch_args` to vsearch_args = "--strand both --usersort"
#' @param vsearch_args (default : "--strand both") a one length character element defining other parameters to
#' passed on to vsearch.
#' @param keep_temporary_files (logical, default: FALSE) Do we keep temporary files ?
#' - temp.fasta (refseq in fasta or dna_seq sequences)
#' - cluster.fasta (centroid if method = "vsearch")
#' - temp.uc (clusters if method = "vsearch")
#'
#' @seealso [asv2otu()], [swarm_clustering()]
#' @details This function use the [merge_taxa_vec()] function to
#' merge taxa into clusters. By default tax_adjust = 0. See the man page
#' of [merge_taxa_vec()].
#'
#' @return A new object of class `physeq` or a list of cluster if dna_seq
#' args was used.
#'
#' @references
#' VSEARCH can be downloaded from
#' \url{https://github.com/torognes/vsearch}.
#' More information in the associated publication
#' \url{https://pubmed.ncbi.nlm.nih.gov/27781170}.
#' @export
#' @author Adrien Taudière
#'
#' @examplesIf MiscMetabar::is_vsearch_installed()
#' \donttest{
#' summary_plot_pq(data_fungi)
#' d_vs <- vsearch_clustering(data_fungi)
#' summary_plot_pq(d_vs)
#' }
#' @details
#' This function is mainly a wrapper of the work of others.
#' Please cite [vsearch](https://github.com/torognes/vsearch).
vsearch_clustering <- function(physeq = NULL,
dna_seq = NULL,
nproc = 1,
id = 0.97,
vsearchpath = "vsearch",
tax_adjust = 0,
vsearch_cluster_method = "--cluster_size",
vsearch_args = "--strand both",
keep_temporary_files = FALSE) {
dna <- physeq_or_string_to_dna(physeq = physeq, dna_seq = dna_seq)
Biostrings::writeXStringSet(dna, paste0(tempdir(), "/", "temp.fasta"))
system2(
vsearchpath,
paste0(
paste0(
" ",
vsearch_cluster_method,
" ",
paste0(tempdir(), "/", "temp.fasta"),
" ",
vsearch_args
),
" -id ",
id,
" --centroids ",
paste0(tempdir(), "/", "cluster.fasta"),
" --uc ",
paste0(tempdir(), "/", "temp.uc")
),
stdout = TRUE,
stderr = TRUE
)
pack_clusts <-
utils::read.table(paste0(tempdir(), "/", "temp.uc"), sep = "\t")
colnames(pack_clusts) <-
c(
"type",
"cluster",
"width",
"identity",
"strand",
"6",
"7",
"cigarAlignment",
"query",
"target"
)
clusters <- pack_clusts$cluster[pack_clusts$type != "C"]
names(clusters) <- pack_clusts$query[pack_clusts$type != "C"]
clusters <- clusters[match(taxa_names(physeq), names(clusters))]
if (inherits(physeq, "phyloseq")) {
new_obj <-
merge_taxa_vec(physeq,
clusters,
tax_adjust = tax_adjust
)
} else if (inherits(dna_seq, "character")) {
new_obj <- pack_clusts
} else {
stop(
"You must set the args physeq (object of class phyloseq) or dna_seq (character vector)."
)
}
if (file.exists(paste0(tempdir(), "/", "temp.fasta")) &&
!keep_temporary_files) {
unlink(paste0(tempdir(), "/", "temp.fasta"))
}
if (file.exists(paste0(tempdir(), "/", "cluster.fasta")) &&
!keep_temporary_files) {
unlink(paste0(tempdir(), "/", "cluster.fasta"))
}
if (file.exists(paste0(tempdir(), "/", "temp.uc")) &&
!keep_temporary_files) {
unlink(paste0(tempdir(), "/", "temp.uc"))
}
return(new_obj)
}
###############################################################################
################################################################################
#' Search for a list of sequence in an object to remove chimera taxa
#' using [vsearch](https://github.com/torognes/vsearch)
#'
#' `r lifecycle::badge("experimental")`
#'
#' @param object (required) A phyloseq-class object or one of dada, derep,
#' data.frame or list coercible to sequences table using the
#' function [dada2::makeSequenceTable()]
#' @param type (default "Discard_only_chim"). The type define the type of
#' filtering.
#'
#' - "Discard_only_chim" will only discard taxa classify as chimera by vsearch
#' - "Select_only_non_chim" will only select taxa classify as non-chimera by
#' vsearch(after filtering taxa based on their sequence length by the
#' parameter `min_seq_length` from the [chimera_detection_vs()] function)
#' - "Select_only_chim" will only select taxa classify as chimera by
#' vsearch (after filtering taxa based on their sequence length by the
#' parameter `min_seq_length` from the [chimera_detection_vs()] function)
#' @param clean_pq (logical; default FALSE) If TRUE, return the phyloseq object
#' after cleaning using the default parameter of [clean_pq()] function.
#'
#' @param ... Others arguments passed on to [chimera_detection_vs()] function
#' @seealso [chimera_detection_vs()]
#' @return
#'
#' - I/ a sequences tables if object is of class dada, derep, data.frame or
#' list.
#' - II/ a phyloseq object without (or with if type = 'Select_only_chim')
#' chimeric taxa
#'
#' @export
#'
#' @examplesIf MiscMetabar::is_vsearch_installed()
#' \donttest{
#' data_fungi_nochim <- chimera_removal_vs(data_fungi)
#' data_fungi_nochim_16 <- chimera_removal_vs(data_fungi,
#' abskew = 16,
#' min_seq_length = 10
#' )
#' data_fungi_nochim2 <-
#' chimera_removal_vs(data_fungi, type = "Select_only_non_chim")
#' data_fungi_chimera <-
#' chimera_removal_vs(data_fungi, type = "Select_only_chim")
#' }
#' @author Adrien Taudière
#' @details
#' This function is mainly a wrapper of the work of others.
#' Please make [vsearch](https://github.com/torognes/vsearch).
chimera_removal_vs <-
function(object,
type = "Discard_only_chim",
clean_pq = FALSE,
...) {
if (inherits(object, "dada") ||
inherits(object, "derep") ||
inherits(object, "data.frame") ||
inherits(object, "list")) {
object <- makeSequenceTable(object)
}
if (inherits(object, "matrix")) {
chim_detect <-
chimera_detection_vs(
seq2search = colnames(object),
nb_seq = colSums(object),
...
)
if (type == "Discard_only_chim") {
seq_tab_final <-
object[, !colnames(object) %in% as.character(chim_detect$chimera)]
} else if (type == "Select_only_non_chim") {
seq_tab_final <- seq_tab_Pairs[, as.character(chim_rm$non_chimera)]
} else if (type == "Select_only_chim") {
seq_tab_final <- seq_tab_Pairs[, as.character(chim_rm$chimera)]
} else {
stop(
"Type must be set to one of 'Discard_only_chim',
'Select_only_non_chim', or 'Select_only_chim'"
)
}
seq_tab_final <- seq_tab_final
return(seq_tab_final)
} else if (inherits(object, "phyloseq")) {
verify_pq(object)
if (sum(taxa_sums(object) == 0) > 0) {
object <- clean_pq(object)
}
chim_detect <-
chimera_detection_vs(
seq2search = refseq(object),
nb_seq = taxa_sums(object),
...
)
if (type == "Discard_only_chim") {
cond <-
!as.character(refseq(object)) %in% as.character(chim_detect$chimera)
names(cond) <- names(refseq(object))
new_physeq <-
subset_taxa_pq(object, condition = cond)
} else if (type == "Select_only_non_chim") {
cond <-
as.character(refseq(object)) %in% as.character(chim_detect$non_chimera)
names(cond) <- names(refseq(object))
new_physeq <-
subset_taxa_pq(object, condition = cond)
} else if (type == "Select_only_chim") {
cond <-
as.character(refseq(object)) %in% as.character(chim_detect$chimera)
names(cond) <- names(refseq(object))
new_physeq <-
subset_taxa_pq(object, condition = cond)
} else {
stop(
"Type must be set to one of 'Discard_only_chim',
'Select_only_non_chim', or 'Select_only_chim'"
)
}
if (clean_pq) {
new_physeq <- clean_pq(physeq)
}
return(new_physeq)
}
}
#' Detect for chimera taxa using [vsearch](https://github.com/torognes/vsearch)
#'
#' `r lifecycle::badge("experimental")`
#'
#'
#' @param seq2search (required) a list of DNA sequences coercible by function
#' [Biostrings::DNAStringSet()]
#' @param nb_seq (required) a numeric vector giving the number of sequences for
#' each DNA sequences
#' @param vsearchpath (default: vsearch) path to vsearch
#' @param abskew (int, default 2) The abundance skew is used to distinguish in a
#' three way alignment which sequence is the chimera and which are the
#' parents. The assumption is that chimeras appear later in the PCR
#' amplification process and are therefore less abundant than their parents.
#' The default value is 2.0, which means that the parents should be at least
#' 2 times more abundant than their chimera. Any positive value equal or
#' greater than 1.0 can be used.
#' @param min_seq_length (int, default 100)) Minimum length of sequences to
#' be part of the analysis
#' @param vsearch_args (default "--fasta_width 0") A list of other args for
#' vsearch command
#' @param keep_temporary_files (logical, default: FALSE) Do we keep temporary
#' files ?
#' - non_chimeras.fasta
#' - chimeras.fasta
#' - borderline.fasta
#'
#' @return A list of 3 including non-chimera taxa (`$non_chimera`), chimera taxa
#' (`$chimera`) and bordeline taxa (`$borderline`)
#' @export
#'
#' @examplesIf MiscMetabar::is_vsearch_installed()
#' \donttest{
#' chimera_detection_vs(
#' seq2search = data_fungi@refseq,
#' nb_seq = taxa_sums(data_fungi)
#' )
#' }
#' @author Adrien Taudière
#' @details
#' This function is mainly a wrapper of the work of others.
#' Please make [vsearch](https://github.com/torognes/vsearch).
chimera_detection_vs <- function(seq2search,
nb_seq,
vsearchpath = "vsearch",
abskew = 2,
min_seq_length = 100,
vsearch_args = "--fasta_width 0",
keep_temporary_files = FALSE) {
dna_raw <- Biostrings::DNAStringSet(seq2search)
names(dna_raw) <- paste0(
"ASV", seq(1, length(seq2search)),
";size=", nb_seq
)
dna <- dna_raw[Biostrings::width(dna_raw) >= min_seq_length]
abun <- unlist(strsplit(names(dna), split = "="))
abun_tot <-
sum(as.numeric(abun[seq(2, 2 * length(abun), by = 2)]), na.rm = T)
message(
paste(
"Filtering for sequences under",
min_seq_length,
"bp remove a total of",
length(dna_raw) - length(dna),
"(",
round((length(dna_raw) - length(dna)) / length(dna_raw) * 100, 2),
"%)",
"unique sequences for a total of",
sum(nb_seq) - abun_tot,
"sequences removed",
"(",
round((sum(nb_seq) - abun_tot) / sum(nb_seq) * 100, 2),
"%)"
)
)
Biostrings::writeXStringSet(
dna,
paste0(tempdir(), "/", "temp.fasta")
)
system2(
vsearchpath,
paste0(
" --uchime_denovo ",
paste0(tempdir(), "/", "temp.fasta"),
" --abskew ",
abskew,
" --nonchimeras ",
paste0(tempdir(), "/", "non_chimeras.fasta"),
" --chimeras ",
paste0(tempdir(), "/", "chimeras.fasta"),
" --borderline ",
paste0(tempdir(), "/", "borderline.fasta"),
" ",
vsearch_args
),
stdout = TRUE,
stderr = TRUE
)
non_chimera_AAStringSet <-
Biostrings::readAAStringSet(paste0(tempdir(), "/", "non_chimeras.fasta"))
chimera_AAStringSet <-
Biostrings::readAAStringSet(paste0(tempdir(), "/", "chimeras.fasta"))
borderline_AAStringSet <-
Biostrings::readAAStringSet(paste0(tempdir(), "/", "borderline.fasta"))
if (!keep_temporary_files) {
if (file.exists(paste0(tempdir(), "temp.fasta"))) {
unlink(paste0(tempdir(), "temp.fasta"))
}
if (file.exists(paste0(tempdir(), "non_chimeras.fasta"))) {
unlink(paste0(tempdir(), "non_chimeras.fasta"))
}
if (file.exists(paste0(tempdir(), "chimeras.fasta"))) {
unlink(paste0(tempdir(), "chimeras.fasta"))
}
} else {
message(paste0("Temporary files are located at ", tempdir()))
}
return(
list(
"non_chimera" = non_chimera_AAStringSet,
"chimera" = chimera_AAStringSet,
"borderline" = borderline_AAStringSet
)
)
}
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