R/util.R

In brendanf/tzara: Cluster long amplicons using dada2 denoising on variable regions

# copy of coerce code from LSUx, since it is not required for tzara

#' @importClassesFrom Biostrings DNAStringSet
#' @importClassesFrom ShortRead ShortRead

methods::setAs(
    "DNAStringSet",
    "ShortRead",
    function(from) {
        ShortRead::ShortRead(
            magrittr::set_names(from, NULL),
            Biostrings::BStringSet(names(from))
        )
    }
)



methods::setAs(
    "ShortRead",
    "DNAStringSet",
    function(from) {
        out <- ShortRead::sread(from)
        names(out) <- as.character(ShortRead::id(from))
        out
    }
)



methods::setAs(
    "character",
    "ShortRead",
    function(from) {
        if (length(from) == 1 && file.exists(from)) {
            from <- tryCatch(
                ShortRead::readFasta(from),
                error = function(e) {
                    ShortRead::readFastq(from)
                }
            )
        } else {
            ShortRead::ShortRead(
                sread = Biostrings::DNAStringSet(from, use.names = FALSE),
                id = Biostrings::BStringSet(names(from))
            )
        }
    }
)



methods::setAs(
    "ShortRead",
    "character",
    function(from) {
        out <- as.character(ShortRead::sread(from))
        names(out) <- as.character(ShortRead::id(from))
        out
    }
)


sreadq_to_qsDNAss <- function(from) {
    quality <- Biostrings::quality(from)
    if (methods::is(quality, "FastqQuality")) {
        quality <- methods::as(quality, "PhredQuality")
    } else if (methods::is(quality, "SFastqQuality")) {
        quality <- methods::as(quality, "SolexaQuality")
    }
    to = Biostrings::QualityScaledDNAStringSet(
        x = ShortRead::sread(from),
        quality = quality
    )
    names(to) <- ShortRead::id(from)
    to
}


#' @importClassesFrom Biostrings QualityScaledXStringSet
#' @importClassesFrom ShortRead ShortReadQ

methods::setAs(
    "ShortReadQ",
    "QualityScaledXStringSet",
    sreadq_to_qsDNAss
)


methods::setAs(
    "ShortReadQ",
    "QualityScaledDNAStringSet",
    sreadq_to_qsDNAss
)


qsDNAss_to_sreadq <- function(from) {
    ShortRead::ShortReadQ(
        sread = magrittr::set_names(methods::as(from, "DNAStringSet"), NULL),
        quality = Biostrings::quality(from),
        id = Biostrings::BStringSet(names(from))
    )
}

#' @importClassesFrom Biostrings QualityScaledDNAStringSet


methods::setAs(
    "QualityScaledDNAStringSet",
    "ShortReadQ",
    qsDNAss_to_sreadq
)




methods::setAs(
    "QualityScaledDNAStringSet",
    "ShortRead",
    qsDNAss_to_sreadq
)