R/makeTxDb.R

Defines functions supportedMiRBaseBuildValues makeToyTxDb makeTxDb .foreign_transcripts_warning_msg .foreign_transcripts_stop_msg .a_sample_of_foreign_transcripts_as_one_string .write_cds .write_exons .write_transcripts .write_metadata_table .write_gene_table .write_splicing_table .write_feature_table .write_chrominfo_table .make_splicings_internal_cds_id .make_splicings_internal_exon_id .make_transcripts_internal_tx_id .infer_chrominfo_from_transcripts_and_splicings .makeTxDb_normarg_chrominfo .makeTxDb_normarg_genes .makeTxDb_normarg_splicings .makeTxDb_normarg_transcripts .check_foreign_key .graceful_as_integer .is_character_or_factor .all_logical_NAs

Documented in makeTxDb supportedMiRBaseBuildValues

### =========================================================================
### Making TxDb objects
### -------------------------------------------------------------------------


### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### 1st group of helper functions for makeTxDb()
###
### 4 functions to check and normalize the input of makeTxDb():
###   o .makeTxDb_normarg_transcripts()
###   o .makeTxDb_normarg_splicings()
###   o .makeTxDb_normarg_genes()
###   o .makeTxDb_normarg_chrominfo()
### 1 function to infer the chrominfo table:
###   o .infer_chrominfo_from_transcripts_and_splicings

.all_logical_NAs <- function(x)
{
    is.logical(x) && all(is.na(x))
}

### Also returns TRUE if 'x' is a logical vector of NAs.
.is_character_or_factor <- function(x)
{
    is.character(x) || is.factor(x) || .all_logical_NAs(x)
}

### Like as.integer(x) but fail if 'x' is not a numeric vector or a logical
### vector of NAs.
.graceful_as_integer <- function(x, x_what="x")
{
    if (!(is.numeric(x) || .all_logical_NAs(x)))
        stop(wmsg("'", x_what, "' must be either all NAs ",
                  "or an integer vector"))
    if (!is.integer(x))
        x <- as.integer(x)
    x
}

.check_foreign_key <- function(referring_vals,
                               referring_type,
                               referring_colname,
                               referred_vals,
                               referred_type,
                               referred_colname)
{
    if (!is.na(referring_type) && !is(referring_vals, referring_type))
        stop(wmsg("'", referring_colname, "' must be ",
                  "of type ", referring_type))
    if (!is.na(referred_type) && !is(referred_vals, referred_type))
        stop(wmsg("'", referred_colname, "' must be ",
                  "of type ", referred_type))
    if (any(is.na(referring_vals)))
        stop(wmsg("'", referring_colname, "' cannot contain NAs"))
    if (!all(referring_vals %in% referred_vals))
        stop(wmsg("all the values in '", referring_colname, "' must ",
                  "be present in '", referred_colname, "'"))
}

.makeTxDb_normarg_transcripts <- function(transcripts)
{
    .REQUIRED_COLS <- c("tx_id", "tx_chrom", "tx_strand", "tx_start", "tx_end")
    .OPTIONAL_COLS <- c("tx_name", "tx_type", "gene_id")
    check_colnames(transcripts, .REQUIRED_COLS, .OPTIONAL_COLS, "transcripts")
    ## Check 'tx_id'.
    if (!is.integer(transcripts$tx_id) || any(is.na(transcripts$tx_id)))
        stop(wmsg("'transcripts$tx_id' must be an integer vector ",
                  "with no NAs"))
    if (any(duplicated(transcripts$tx_id)))
        stop(wmsg("'transcripts$tx_id' contains duplicated values"))
    ## Check 'tx_chrom'.
    if (!.is_character_or_factor(transcripts$tx_chrom)
     || any(is.na(transcripts$tx_chrom)))
        stop(wmsg("'transcripts$tx_chrom' must be a character vector ",
                  "(or factor) with no NAs"))
    ## Check 'tx_strand'.
    if (!.is_character_or_factor(transcripts$tx_strand)
     || any(is.na(transcripts$tx_strand)))
        stop(wmsg("'transcripts$tx_strand' must be a character vector ",
                  "(or factor) with no NAs"))
    if (!all(transcripts$tx_strand %in% c("+", "-")))
        stop(wmsg("values in 'transcripts$tx_strand' must be \"+\" or \"-\""))
    ## Check 'tx_start'.
    if (!is.numeric(transcripts$tx_start)
     || any(is.na(transcripts$tx_start)))
        stop(wmsg("'transcripts$tx_start' must be an integer vector ",
                  "with no NAs"))
    if (!is.integer(transcripts$tx_start))
        transcripts$tx_start <- as.integer(transcripts$tx_start)
    ## Check 'tx_end'.
    if (!is.numeric(transcripts$tx_end)
     || any(is.na(transcripts$tx_end)))
        stop(wmsg("'transcripts$tx_end' must be an integer vector ",
                  "with no NAs"))
    if (!is.integer(transcripts$tx_end))
        transcripts$tx_end <- as.integer(transcripts$tx_end)
    ## Check 'tx_start <= tx_end'.
    if (any(transcripts$tx_start > transcripts$tx_end))
        stop(wmsg("transcript starts must be <= transcript ends"))
    ## Check 'tx_name'.
    if (has_col(transcripts, "tx_name")
     && !.is_character_or_factor(transcripts$tx_name))
        stop(wmsg("'transcripts$tx_name' must be a character vector ",
                  "(or factor)"))
    ## Check 'tx_type'.
    if (has_col(transcripts, "tx_type")
     && !.is_character_or_factor(transcripts$tx_type))
        stop(wmsg("'transcripts$tx_type' must be a character vector ",
                  "(or factor)"))
    ## Check 'gene_id'.
    if (has_col(transcripts, "gene_id")
     && !.is_character_or_factor(transcripts$gene_id))
        stop(wmsg("'transcripts$gene_id' must be a character vector ",
                  "(or factor)"))
    transcripts
}

.makeTxDb_normarg_splicings <- function(splicings, transcripts_tx_id)
{
    .REQUIRED_COLS <- c("tx_id", "exon_rank", "exon_start", "exon_end")
    .OPTIONAL_COLS <- c("exon_id", "exon_name", "exon_chrom", "exon_strand",
                        "cds_id", "cds_name", "cds_start", "cds_end",
                        "cds_phase")
    check_colnames(splicings, .REQUIRED_COLS, .OPTIONAL_COLS, "splicings")
    ## Check 'tx_id'.
    .check_foreign_key(splicings$tx_id, "integer", "splicings$tx_id",
                       transcripts_tx_id, "integer", "transcripts$tx_id")
    ## Check 'exon_rank'.
    if (!is.numeric(splicings$exon_rank)
     || any(is.na(splicings$exon_rank)))
        stop(wmsg("'splicings$exon_rank' must be an integer vector ",
                  "with no NAs"))
    if (!is.integer(splicings$exon_rank))
        splicings$exon_rank <- as.integer(splicings$exon_rank)
    if (any(splicings$exon_rank <= 0L))
        stop(wmsg("'splicings$exon_rank' contains non-positive values"))
    ## Check uniqueness of (tx_id, exon_rank) pairs.
    if (any(duplicatedIntegerPairs(splicings$tx_id,
                                               splicings$exon_rank)))
        stop(wmsg("'splicings' must contain unique (tx_id, exon_rank) pairs"))
    ## Check 'exon_id'.
    if (has_col(splicings, "exon_id")
     && (!is.integer(splicings$exon_id) || any(is.na(splicings$exon_id))))
        stop(wmsg("'splicings$exon_id' must be an integer vector ",
                  "with no NAs"))
    ## Check 'exon_name'.
    if (has_col(splicings, "exon_name")
     && !.is_character_or_factor(splicings$exon_name))
        stop(wmsg("'splicings$exon_name' must be a character vector ",
                  "(or factor)"))
    ## Check 'exon_chrom'.
    if (has_col(splicings, "exon_chrom")
     && (!.is_character_or_factor(splicings$exon_chrom)
         || any(is.na(splicings$exon_chrom))))
        stop(wmsg("'splicings$exon_chrom' must be a character vector ",
                  "(or factor) with no NAs"))
    ## Check 'exon_strand'.
    if (has_col(splicings, "exon_strand")
     && (!.is_character_or_factor(splicings$exon_strand)
         || any(is.na(splicings$exon_strand))))
        stop(wmsg("'splicings$exon_strand' must be a character vector ",
                  "(or factor) with no NAs"))
    if (has_col(splicings, "exon_chrom") && !has_col(splicings, "exon_strand"))
        stop(wmsg("if 'splicings' has an \"exon_chrom\" col then ",
                  "it must have an \"exon_strand\" col too"))
    ## Check 'exon_start'.
    if (!is.numeric(splicings$exon_start)
     || any(is.na(splicings$exon_start)))
        stop(wmsg("'splicings$exon_start' must be an integer vector ",
                  "with no NAs"))
    if (!is.integer(splicings$exon_start))
        splicings$exon_start <- as.integer(splicings$exon_start)
    ## Check 'exon_end'.
    if (!is.numeric(splicings$exon_end)
     || any(is.na(splicings$exon_end)))
        stop(wmsg("'splicings$exon_end' must be an integer vector ",
                  "with no NAs"))
    if (!is.integer(splicings$exon_end))
        splicings$exon_end <- as.integer(splicings$exon_end)
    ## Check 'exon_start <= exon_end'.
    if (any(splicings$exon_start > splicings$exon_end))
        stop(wmsg("exon starts must be <= exon ends"))
    ## Check presence of 'cds_start' and 'cds_end'.
    if (has_col(splicings, "cds_start") != has_col(splicings, "cds_end"))
        stop(wmsg("'splicings' has a \"cds_start\" col ",
                  "but no \"cds_end\" col, or vice versa"))
    if (!has_col(splicings, "cds_start")) {
        warning(wmsg("making a TxDb object without CDS information"))
    } else {
        ## Check 'cds_start'.
        splicings$cds_start <- .graceful_as_integer(splicings$cds_start,
                                                    "splicings$cds_start")
        ## Check 'cds_end'.
        splicings$cds_end <- .graceful_as_integer(splicings$cds_end,
                                                  "splicings$cds_end")
        ## Check 'cds_start' and 'cds_end' compatibility.
        if (!all(is.na(splicings$cds_start) == is.na(splicings$cds_end)))
            stop(wmsg("NAs in 'splicings$cds_start' and 'splicings$cds_end' ",
                      "must occur at the same positions"))
        if (any(splicings$cds_start > splicings$cds_end, na.rm=TRUE))
            stop(wmsg("cds starts must be <= cds ends"))
        ## Check CDS and exon compatibility.
        if (any(splicings$cds_start < splicings$exon_start, na.rm=TRUE)
         || any(splicings$cds_end > splicings$exon_end, na.rm=TRUE))
            stop(wmsg("cds starts/ends are incompatible ",
                      "with exon starts/ends"))
    }
    ## Check 'cds_id'.
    if (has_col(splicings, "cds_id")) {
        if (!has_col(splicings, "cds_start"))
            stop(wmsg("'splicings' has a \"cds_id\" col ",
                      "but no \"cds_start\"/\"cds_end\" cols"))
        if (!is.integer(splicings$cds_id))
            stop(wmsg("'splicings$cds_id' must be an integer vector"))
        if (!all(is.na(splicings$cds_id) == is.na(splicings$cds_start)))
            stop(wmsg("NAs in 'splicings$cds_id' don't match those ",
                      "in 'splicings$cds_start' and 'splicings$cds_end'"))
    }
    ## Check 'cds_name'.
    if (has_col(splicings, "cds_name")) {
        if (!has_col(splicings, "cds_start"))
            stop(wmsg("'splicings' has a \"cds_name\" col ",
                      "but no \"cds_start\"/\"cds_end\" cols"))
        if (!.is_character_or_factor(splicings$cds_name))
            stop(wmsg("'splicings$cds_name' must be a character vector ",
                      "(or factor)"))
        if (any(is.na(splicings$cds_name) < is.na(splicings$cds_start)))
            stop(wmsg("'splicings$cds_name' must contain NAs at least ",
                      "where 'splicings$cds_start' and 'splicings$cds_end' ",
                      "contain them"))
    }
    ## Check 'cds_phase'.
    if (has_col(splicings, "cds_phase")) {
        if (!has_col(splicings, "cds_start"))
            stop(wmsg("'splicings' has a \"cds_phase\" col ",
                      "but no \"cds_start\"/\"cds_end\" cols"))
        splicings$cds_phase <- .graceful_as_integer(splicings$cds_phase,
                                                    "splicings$cds_phase")
        if (!all(is.na(splicings$cds_phase) >= is.na(splicings$cds_start)))
            stop(wmsg("NAs in 'splicings$cds_phase' don't match those ",
                      "in 'splicings$cds_start' and 'splicings$cds_end'"))
    }
    splicings
}

.makeTxDb_normarg_genes <- function(genes, transcripts_tx_id,
                                    transcripts_tx_name=NULL)
{
    if (is.null(genes)) {
        genes <- data.frame(tx_id=transcripts_tx_id[FALSE],
                            gene_id=character(0),
                            check.names=FALSE, stringsAsFactors=FALSE)
        return(genes)
    }
    .REQUIRED_COLS <- "gene_id"
    .OPTIONAL_COLS <- c("tx_id", "tx_name")
    check_colnames(genes, .REQUIRED_COLS, .OPTIONAL_COLS, "genes")
    ## Check 'gene_id'.
    if (!.is_character_or_factor(genes$gene_id)
     || any(is.na(genes$gene_id)))
        stop(wmsg("'genes$gene_id' must be a character vector (or factor) ",
                  "with no NAs"))
    ## 'genes' must have one of the 2 optional cols but not both.
    if (length(intersect(colnames(genes), .OPTIONAL_COLS)) != 1L)
        stop(wmsg("'genes' must have either a \"tx_id\" ",
                  "or a \"tx_name\" col but not both"))
    if (!has_col(genes, "tx_id")) {
        ## Remap 'gene_id' to 'tx_id'.
        if (is.null(transcripts_tx_name))
            stop(wmsg("cannot map genes to transcripts, ",
                      "need 'transcripts$tx_name'"))
        names(transcripts_tx_id) <- transcripts_tx_name
        genes <- joinDataFrameWithName2Val(genes, "tx_name",
                                           transcripts_tx_id, "tx_id")
    } else {
        ## Check 'tx_id'.
        .check_foreign_key(genes$tx_id, "integer", "genes$tx_id",
                           transcripts_tx_id, "integer", "transcripts$tx_id")
    }
    genes
}

.makeTxDb_normarg_chrominfo <- function(chrominfo)
{
    .REQUIRED_COLS <- c("chrom", "length")
    .OPTIONAL_COLS <- "is_circular"
    check_colnames(chrominfo, .REQUIRED_COLS, .OPTIONAL_COLS, "chrominfo")
    ## Check 'chrom'.
    if (!.is_character_or_factor(chrominfo$chrom)
     || any(is.na(chrominfo$chrom)))
        stop(wmsg("'chrominfo$chrom' must be a character vector ",
                  "(or factor) with no NAs"))
    if (any(duplicated(chrominfo$chrom)))
        stop(wmsg("'chrominfo$chrom' contains duplicated values"))
    ## Check 'length'.
    chrominfo$length <- .graceful_as_integer(chrominfo$length,
                                             "chrominfo$length")
    na_idx <- is.na(chrominfo$length)
    if (any(na_idx) && !all(na_idx))
        stop(wmsg("'chrominfo$length' cannot mix NAs and non-NAs"))
    ## Check 'is_circular'.
    if (!has_col(chrominfo, "is_circular")) {
        warning(wmsg("chromosome circularity flags ",
                     "are not available for this TxDb object"))
        chrominfo$is_circular <- rep.int(NA, nrow(chrominfo))
    } else if (!is.logical(chrominfo$is_circular)) {
        stop(wmsg("'chrominfo$is_circular' must be a logical vector"))
    }
    chrominfo
}

.infer_chrominfo_from_transcripts_and_splicings <-
    function(transcripts_tx_chrom, splicings_exon_chrom)
{
    warning(wmsg("chromosome lengths and circularity flags ",
                 "are not available for this TxDb object"))
    chrom <- unique(c(as.character(transcripts_tx_chrom),
                      as.character(splicings_exon_chrom)))
    chrom_ids <- rankSeqlevels(chrom)
    chrom[chrom_ids] <- chrom
    data.frame(
        chrom=chrom,
        length=rep.int(NA_integer_, length(chrom)),
        is_circular=rep.int(NA, length(chrom)),
        check.names=FALSE, stringsAsFactors=FALSE
    )
}


### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### 2nd group of helper functions for makeTxDb()
###
### These functions deal with id assignment and reassignment.
###

.make_transcripts_internal_tx_id <- function(transcripts, reassign.ids,
                                             chrominfo_chrom)
{
    if (!reassign.ids)
        return(transcripts$tx_id)
    chrom_ids <- match(transcripts$tx_chrom, chrominfo_chrom)
    makeFeatureIds(chrom_ids, transcripts$tx_strand,
                   transcripts$tx_start,
                   transcripts$tx_end,
                   name=transcripts$tx_name,
                   type=transcripts$tx_type)
}

.make_splicings_internal_exon_id <- function(splicings, reassign.ids,
                                             chrominfo_chrom)
{
    if (!reassign.ids && has_col(splicings, "exon_id"))
        return(splicings$exon_id)
    chrom_ids <- match(splicings$exon_chrom, chrominfo_chrom)
    makeFeatureIds(chrom_ids, splicings$exon_strand,
                   splicings$exon_start,
                   splicings$exon_end,
                   name=splicings$exon_name,
                   same.id.for.dups=TRUE)
}

.make_splicings_internal_cds_id <- function(splicings, reassign.ids,
                                            chrominfo_chrom)
{
    if (!reassign.ids && has_col(splicings, "cds_id"))
        return(splicings$cds_id)
    ans <- rep.int(NA_integer_, nrow(splicings))
    if (has_col(splicings, "cds_start")) {
        not_NA <- !is.na(splicings$cds_start)
        chrom_ids <- match(splicings$exon_chrom, chrominfo_chrom)
        ids <- makeFeatureIds(chrom_ids[not_NA],
                              splicings$exon_strand[not_NA],
                              splicings$cds_start[not_NA],
                              splicings$cds_end[not_NA],
                              name=splicings$cds_name[not_NA],
                              same.id.for.dups=TRUE)
        ans[not_NA] <- ids
    }
    ans
}


### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### 3rd group of helper functions for makeTxDb()
###
### These functions deal with writing data to the database.
###

.write_chrominfo_table <- function(conn, chrominfo)
{
    data <- data.frame(
        internal_chrom_id=seq_len(nrow(chrominfo)),
        chrom=as.character(chrominfo$chrom),
        length=chrominfo$length,
        is_circular=chrominfo$is_circular,
        check.names=FALSE, stringsAsFactors=FALSE)

    ## Create the table.
    SQL <- build_SQL_CREATE_chrominfo_table()
    dbExecute(conn, SQL)

    ## Fill the table.
    insert_data_into_table(conn, "chrominfo", data)
}

.write_feature_table <- function(conn, table,
                                 internal_id, name, type,
                                 chrom, strand,
                                 start, end)
{
    colnames <- TXDB_table_columns(table)
    if (is.null(name))
        name <- rep.int(NA_character_, length(internal_id))
    data <- data.frame(
        internal_id=internal_id,
        name=name,
        check.names=FALSE, stringsAsFactors=FALSE)
    if ("type" %in% names(colnames)) {
        if (is.null(type))
            type <- rep.int(NA_character_, length(internal_id))
        data$type <- type
    }
    data <- cbind(data,
                  data.frame(
                      chrom=chrom,
                      strand=strand,
                      start=start,
                      end=end,
                      check.names=FALSE, stringsAsFactors=FALSE))
    data <- unique(data)

    ## Create the table.
    SQL <- build_SQL_CREATE_feature_table(table)
    dbExecute(conn, SQL)

    ## Fill the table.
    insert_data_into_table(conn, table, data)
}

.write_splicing_table <- function(conn,
                                  internal_tx_id,
                                  exon_rank,
                                  internal_exon_id,
                                  internal_cds_id,
                                  cds_phase)
{
    if (is.null(cds_phase))
        cds_phase <- rep.int(NA_integer_, length(internal_tx_id))
    data <- data.frame(
        internal_tx_id=internal_tx_id,
        exon_rank=exon_rank,
        internal_exon_id=internal_exon_id,
        internal_cds_id=internal_cds_id,
        cds_phase=cds_phase,
        check.names=FALSE, stringsAsFactors=FALSE)

    ## Create the 'splicing' table and related indices.
    SQL <- build_SQL_CREATE_splicing_table()
    dbExecute(conn, SQL)
    #Temporarily drop the indices.
    #indexed_columns <- c("_tx_id", "_exon_id", "_cds_id")
    #SQL <- paste(sprintf("CREATE INDEX splicing%s ON splicing (%s)",
    #                     indexed_columns, indexed_columns),
    #             collapse="; ")
    #dbExecute(conn, SQL)

    ## Fill the 'splicing' table.
    insert_data_into_table(conn, "splicing", data)
}

.write_gene_table <- function(conn, gene_id, internal_tx_id)
{
    data <- data.frame(
        gene_id=gene_id,
        internal_tx_id=internal_tx_id,
        check.names=FALSE, stringsAsFactors=FALSE)
    data <- unique(data)
    data <- S4Vectors:::extract_data_frame_rows(data, !is.na(data$gene_id))

    ## Create the table.
    SQL <- build_SQL_CREATE_gene_table()
    dbExecute(conn, SQL)

    ## Fill the table.
    insert_data_into_table(conn, "gene", data)
}

.write_metadata_table <- function(conn, metadata)
{
    nb_transcripts <- dbEasyQuery(conn,
                                  "SELECT COUNT(*) FROM transcript")[[1L]]
    thispkg_version <- packageDescription("GenomicFeatures")$Version
    rsqlite_version <- packageDescription("RSQLite")$Version
    mat1 <- matrix(c(
        DB_TYPE_NAME, DB_TYPE_VALUE,
        "Supporting package", "GenomicFeatures"),
        ncol=2, byrow=TRUE
    )
    mat2 <- matrix(c(
        "Nb of transcripts", nb_transcripts,
        "Db created by",     "GenomicFeatures package from Bioconductor",
        "Creation time",     svn.time(),
        "GenomicFeatures version at creation time", thispkg_version,
        "RSQLite version at creation time", rsqlite_version,
        "DBSCHEMAVERSION",   DB_SCHEMA_VERSION),
        ncol=2, byrow=TRUE
    )
    colnames(mat1) <- colnames(mat2) <- c("name", "value")
    metadata <- rbind(data.frame(name=mat1[ , "name"], value=mat1[ , "value"],
                                 check.names=FALSE, stringsAsFactors=FALSE),
                      metadata,
                      data.frame(name=mat2[ , "name"], value=mat2[ , "value"],
                                 check.names=FALSE, stringsAsFactors=FALSE))
    dbWriteTable(conn, "metadata", metadata, row.names=FALSE)
}

.write_transcripts <- function(conn, transcripts, internal_tx_id)
{
    .write_feature_table(conn, "transcript",
        internal_tx_id, transcripts$tx_name, transcripts$tx_type,
        transcripts$tx_chrom, transcripts$tx_strand,
        transcripts$tx_start, transcripts$tx_end)
}

.write_exons <- function(conn, splicings, internal_exon_id)
{
    .write_feature_table(conn, "exon",
        internal_exon_id, splicings$exon_name, NULL,
        splicings$exon_chrom, splicings$exon_strand,
        splicings$exon_start, splicings$exon_end)
}

.write_cds <- function(conn, splicings, internal_cds_id)
{
    not_NA <- !is.na(internal_cds_id)
    internal_cds_id <- internal_cds_id[not_NA]
    if (!has_col(splicings, "cds_start")) {
        cds_name <- cds_chrom <- cds_strand <- character(0)
        cds_start <- cds_end <- integer(0)
    } else {
        cds_name <- splicings$cds_name[not_NA]
        cds_chrom <- splicings$exon_chrom[not_NA]
        cds_strand <- splicings$exon_strand[not_NA]
        cds_start <- splicings$cds_start[not_NA]
        cds_end <- splicings$cds_end[not_NA]
    }
    .write_feature_table(conn, "cds",
        internal_cds_id, cds_name, NULL,
        cds_chrom, cds_strand,
        cds_start, cds_end)
}


### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### makeTxDb().
###

.a_sample_of_foreign_transcripts_as_one_string <-
    function(transcripts_tx_name, foreign_idx)
{
    if (is.null(transcripts_tx_name))
        return("")
    foreign_tx_names <- transcripts_tx_name[foreign_idx]
    foreign_tx_names <- foreign_tx_names[!is.na(foreign_tx_names)]
    if (length(foreign_tx_names) == 0L)
        return("")
    foreign_tx_names <- head(foreign_tx_names, n=4L)
    fmt <- "transcript"
    if (length(foreign_tx_names) >= 2L)
        fmt <- paste0(fmt, "s")
    fmt <- paste0(fmt, " %s")
    if (length(foreign_tx_names) < length(foreign_idx))
        fmt <- paste0("e.g. ", fmt, ", ...")
    fmt <- paste0(" (", fmt, ")")
    sprintf(fmt, paste0(foreign_tx_names, collapse=", "))
}

.foreign_transcripts_stop_msg <- function(transcripts_tx_name, foreign_idx)
{
    msg1 <- if (length(foreign_idx) >= 2L)
                "transcripts are on unknown sequences"
            else
                "transcript is on an unknown sequence"
    msg2 <- .a_sample_of_foreign_transcripts_as_one_string(transcripts_tx_name,
                                                           foreign_idx)
    c(length(foreign_idx), " ", msg1, msg2)
}

.foreign_transcripts_warning_msg <- function(transcripts_tx_name, foreign_idx)
{
    msg1 <- if (length(foreign_idx) >= 2L)
                "transcripts were dropped because they are on unknown sequences"
            else
                "transcript was drop because it is on an unknown sequence"
    msg2 <- .a_sample_of_foreign_transcripts_as_one_string(transcripts_tx_name,
                                                           foreign_idx)
    c(length(foreign_idx), " ", msg1, msg2)
}

makeTxDb <- function(transcripts, splicings,
                     genes=NULL, chrominfo=NULL, metadata=NULL,
                     reassign.ids=FALSE,
                     on.foreign.transcripts=c("error", "drop"))
{
    if (!isTRUEorFALSE(reassign.ids))
        stop(wmsg("'reassign.ids' must be TRUE or FALSE"))
    on.foreign.transcripts <- match.arg(on.foreign.transcripts)

    transcripts <- .makeTxDb_normarg_transcripts(transcripts)
    splicings <- .makeTxDb_normarg_splicings(splicings, transcripts$tx_id)
    if (has_col(transcripts, "gene_id")) {
        if (!is.null(genes))
            stop(wmsg("'genes' must be NULL when 'transcripts' ",
                      "has a \"gene_id\" col"))
        genes <- transcripts[!is.na(transcripts$gene_id),
                             c("tx_id", "gene_id")]
    } else {
        genes <- .makeTxDb_normarg_genes(genes, transcripts$tx_id,
                                   transcripts_tx_name=transcripts$tx_name)
    }
    if (is.null(chrominfo)) {
        chrominfo <- .infer_chrominfo_from_transcripts_and_splicings(
                         transcripts$tx_chrom,
                         splicings$exon_chrom)
    } else {
        chrominfo <- .makeTxDb_normarg_chrominfo(chrominfo)
        ## Look for "foreign transcripts" i.e. for transcripts that are on
        ## sequences not in 'chrominfo'.
        ok <- transcripts$tx_chrom %in% chrominfo$chrom
        foreign_tx <- transcripts[!ok, "tx_id"]
        if (!is.null(splicings$exon_chrom)) {
            ok <- splicings$exon_chrom %in% chrominfo$chrom
            foreign_tx <- union(foreign_tx, splicings[!ok, "tx_id"])
        }
        nb_foreign_tx <- length(foreign_tx)
        if (nb_foreign_tx != 0L) {
            dropped1 <- transcripts$tx_id %in% foreign_tx
            if (on.foreign.transcripts == "error") {
                ## Error if foreign transcripts.
                msg <- .foreign_transcripts_stop_msg(transcripts$tx_name,
                                                     which(dropped1))
                stop(wmsg(msg))
            } else {
                ## Drop foreign transcripts with a warning.
                transcripts <- S4Vectors:::extract_data_frame_rows(
                                   transcripts, !dropped1)
                dropped2 <- splicings$tx_id %in% foreign_tx
                splicings <- S4Vectors:::extract_data_frame_rows(
                                   splicings, !dropped2)
                dropped3 <- genes$tx_id %in% foreign_tx
                genes <- S4Vectors:::extract_data_frame_rows(
                                   genes, !dropped3)
                msg <- .foreign_transcripts_warning_msg(transcripts$tx_name,
                                                        which(dropped1))
                warning(wmsg(msg))
            }
        }
    }
    transcripts_internal_tx_id <- .make_transcripts_internal_tx_id(
                                             transcripts,
                                             reassign.ids,
                                             chrominfo$chrom)
    splicings_internal_tx_id <- translateIds(transcripts$tx_id,
                                             transcripts_internal_tx_id,
                                             splicings$tx_id)
    genes_internal_tx_id <- translateIds(transcripts$tx_id,
                                         transcripts_internal_tx_id,
                                         genes$tx_id)
    ## Infer 'splicings$exon_chrom' and 'splicings$exon_strand' when missing
    ## and generate internal exon id.
    splicings2transcripts <- match(splicings_internal_tx_id,
                                   transcripts_internal_tx_id)
    if (!has_col(splicings, "exon_chrom"))
        splicings$exon_chrom <- transcripts$tx_chrom[splicings2transcripts]
    if (!has_col(splicings, "exon_strand"))
        splicings$exon_strand <- transcripts$tx_strand[splicings2transcripts]
    splicings_internal_exon_id <- .make_splicings_internal_exon_id(
                                             splicings,
                                             reassign.ids,
                                             chrominfo$chrom)
    splicings_internal_cds_id <- .make_splicings_internal_cds_id(
                                             splicings,
                                             reassign.ids,
                                             chrominfo$chrom)
    ## Create the db in a temp file.
    conn <- dbConnect(SQLite(), dbname="")
    .write_chrominfo_table(conn, chrominfo)  # must come first
    .write_transcripts(conn, transcripts, transcripts_internal_tx_id)
    .write_exons(conn, splicings, splicings_internal_exon_id)
    .write_cds(conn, splicings, splicings_internal_cds_id)
    .write_splicing_table(conn,
                          splicings_internal_tx_id,
                          splicings$exon_rank,
                          splicings_internal_exon_id,
                          splicings_internal_cds_id,
                          splicings$cds_phase)
    .write_gene_table(conn, genes$gene_id, genes_internal_tx_id)
    .write_metadata_table(conn, metadata)  # must come last!
    TxDb(conn)
}


### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### makeToyTxDb().
###
### A simple wrapper around makeTxDb() typically used to make toy
### TxDb objects.
###
### 'splicings' must have the same format as for makeTxDb().
### If the "exon_chrom" col is missing, then it's added and filled with
### "chr1". If the "exon_strand" col is missing, then it's added and filled
### with "+". Within each transcript the "exon_chrom" and "exon_strand" values
### of the first and last exons must be the same (otherwise, there would be
### no easy way to infer the 'transcripts' table (see next).
###
### 'transcripts' is "inferred" from 'splicings' as follow:
###   - the "tx_chrom" and "tx_strand" cols are inferred from
###     'splicings$exon_chrom' and 'splicings$exon_strand' using the values
###     of the first exon (exon_rank=1) in the transcript;
###   - the transcripts starts/ends are inferred from the starts/ends of
###     their first and last exons.
###

makeToyTxDb <- function(splicings, genes=NULL)
{
    if (!is.data.frame(splicings))
        stop(wmsg("'splicings' must be a data frame"))
    stop("not ready yet, sorry!")
}


## helper to list mirbase.db miRBaseBuild values for species
supportedMiRBaseBuildValues <- function(){
    loadNamespace("mirbase.db")
    res <- toTable(mirbase.db::mirbaseSPECIES)[,c("name","genome_assembly")]
    S4Vectors:::extract_data_frame_rows(res, res$genome_assembly != "")
}
Bioconductor/GenomicFeatures documentation built on Aug. 29, 2021, 1:03 p.m.