Bedtools

R/cmd-bedtools.R

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+#' Run bedtools
+#'
+#' The `bedtools` is a powerful toolset for genome arithmetic.
+#' @param subcmd Sub-Command of bedtools. Details see: `r rd_help("bedtools")`.
+#' @param file1 Path to bed/gff(gtf)/vcf/bam(sam) file.
+#' @param file2 Path to the second file, some commands require.
+#' @param ... `r rd_dots("bedtools")`.
+#' @param ofile Path to the output file.
+#' @param bedtools `r rd_cmd("bedtools")`.
+#' @seealso
+#' - <https://github.com/arq5x/bedtools2/>
+#'
+#' `r rd_seealso()`
+#' @inherit exec return
+#' @family command
+#' @export
+bedtools <- make_command(
+  "bedtools",
+  function(
+    subcmd = NULL,
+    file1,
+    ofile,
+    ...,
+    file2 = NULL,
+    bedtools = NULL
+  ) {
+    assert_string(subcmd, allow_empty = FALSE, allow_null = TRUE)
+    assert_string(bedtools, allow_empty = FALSE, allow_null = TRUE)
+    BEDTools$new(
+      cmd = bedtools,
+      ...,
+      subcmd = subcmd,
+      file1 = file1,
+      file2 = file2,
+      ofile = ofile
+    )
+  }
+)
+
+BEDTools <- R6Class(
+  "BEDTools",
+  inherit = Command,
+  private = list(
+    alias = function() "bedtools",
+    setup_help_params = function() "help",
+    combine_params = function(subcmd, file1, file2, ofile) {
+      c(
+        if (private$help) {
+          c(super$combine_params(), subcmd)
+        } else {
+          c(subcmd, super$combine_params())
+        },
+        arg0("-a", file1),
+        if (!is.null(file2)) arg0("-b", file2) else NULL,
+        arg0("-o", ofile),
+      )
+    }
+  )
+)

R/cmd-bedtools_1.R

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+#' Run bedtools
+#'
+#' The `bedtools` is a powerful toolset for genome arithmetic,
+#' which includes `intersect`, `merge`, `coverage`, `getfasta`, `closest`, etc.
+#' @param file1 Path to bed/gff(gtf)/vcf/bam(sam) file.
+#' @param file2 Path to the second file, some commands require.
+#' @param ...
+#'  - `bedtools intersect`: `r rd_dots("bedtools intersect")`.
+#'  - `bedtools merge`: `r rd_dots("bedtools merge")`.
+#'  - `bedtools coverage`: `r rd_dots("bedtools coverage")`.
+#'  - `bedtools getfasta`: `r rd_dots("bedtools getfasta")`.
+#'  - `bedtools closest`: `r rd_dots("bedtools closest")`.
+#' @param ofile Path to the output file.
+#' @param
+#'  - `bedtools intersect`: `r rd_cmd("bedtools intersect")`.
+#'  - `bedtools merge`: `r rd_cmd("bedtools merge")`.
+#'  - `bedtools coverage`: `r rd_cmd("bedtools coverage")`.
+#'  - `bedtools getfasta`: `r rd_cmd("bedtools getfasta")`.
+#'  - `bedtools closest`: `r rd_cmd("bedtools closest")`.
+#' @seealso
+#' - <https://github.com/arq5x/bedtools2/>
+#'
+#' `r rd_seealso()`
+#' @inherit exec return
+#' @family command
+#' @export
+#  bedtools_intersect ----
+bedtools_intersect <- make_command(
+  "bedtools_intersect",
+  function(
+    file1,
+    file2,
+    ofile,
+    ...,
+    `bedtools intersect` = NULL
+  ){
+    assert_string(`bedtools intersect`, allow_empty = FALSE, allow_null = TRUE)
+    BEDTools_Intersect$new(
+      cmd = `bedtools intersect`,
+      ...,
+      file1 = file1,
+      file2 = file2,
+      ofile = ofile,
+    )
+  }
+)
+
+BEDTools_Intersect <- R6Class(
+  "BEDTools_Intersect",
+  inherit = Command,
+  private = list(
+    alias = function() "bedtools intersect",
+    setup_help_params = function() "--help",
+    setup_command_params = function(file1, file2, ofile){
+      c(
+        arg0("-a", file1),
+        arg0("-b", file2),
+        arg0("-wa"),
+        arg0("-o", ofile),
+      )
+    }
+  )
+)
+
+#  bedtools_merge ----
+bedtools_merge <- make_command(
+  "bedtools_merge",
+  function(
+    file1,
+    ofile,
+    ...,
+    dist = NULL,
+    `bedtools merge` = NULL
+  ){
+    assert_string(`bedtools merge`, allow_empty = FALSE, allow_null = TRUE)
+    `BEDTools_Merge`$new(
+      cmd = `bedtools merge`,
+      ...,
+      file1 = file1,
+      dist = dist,
+      ofile = ofile,
+    )
+  }
+)
+
+BEDTools_Merge <- R6Class(
+  "BEDTools_Merge",
+  inherit = Command,
+  private = list(
+    alias = function() "bedtools merge",
+    setup_help_params = function() "--help",
+    setup_command_params = function(file1, dist, ofile){
+      c(
+        if (endsWith(file1, ".bed")|endsWith(file1, ".gff")){
+          arg0("-i", file1)
+        } else{
+          cli::cli_abort(
+            "{.arg file1} must be BED/GFF"
+          )
+        },
+        if (!is.null(dist)) arg0("-d", dist) else NULL,
+        arg0("-o", ofile),
+      )
+    }
+  )
+)
+
+#  bedtools_coverage ----
+bedtools_coverage <- make_command(
+  "bedtools_coverage",
+  function(
+    file1,
+    file2,
+    ofile,
+    ...,
+    `bedtools coverage` = NULL
+  ){
+    assert_string(`bedtools coverage`, allow_empty = FALSE, allow_null = TRUE)
+    BEDTools_Coverage$new(
+      cmd = `bedtools coverage`,
+      ...,
+      file1 = file1,
+      file2 = file2,
+      ofile = ofile,
+    )
+  }
+)
+
+BEDTools_Coverage <- R6Class(
+  "BEDTools_Coverage",
+  inherit = Command,
+  private = list(
+    alias = function() "bedtools coverage",
+    setup_help_params = function() "--help",
+    setup_command_params = function(file1, file2, ofile){
+      c(
+        if (endsWith(file1, ".bed")|endsWith(file1, ".gff")){
+          arg0("-a", file1)
+        } else{
+          cli::cli_abort(
+            "{.arg file1} must be BED/GFF"
+          )
+        },
+        if (endsWith(file2, ".bed")|endsWith(file2, ".gff")|endsWith(file2, ".bam")){
+          arg0("-b", file2)
+        } else{
+          cli::cli_abort(
+            "{.arg file2} must be BED/GFF/BAM"
+          )
+        },
+        arg0("-o", ofile),
+      )
+    }
+  )
+)
+
+#  bedtools_getfasta ----
+bedtools_getfasta <- make_command(
+  "bedtools_getfasta",
+  function(
+    file1,
+    file2,
+    ofile,
+    ...,
+    `bedtools getfasta` = NULL
+  ){
+    assert_string(`bedtools getfasta`, allow_empty = FALSE, allow_null = TRUE)
+    BEDTools_Getfasta$new(
+      cmd = `bedtools getfasta`,
+      ...,
+      file1 = file1,
+      file2 = file2,
+      ofile = ofile,
+    )
+  }
+)
+
+BEDTools_Getfasta <- R6Class(
+  "BEDTools_Getfasta",
+  inherit = Command,
+  private = list(
+    alias = function() "bedtools getfasta",
+    setup_help_params = function() "--help",
+    setup_command_params = function(file1, file2, ofile){
+      c(
+        if (endsWith(file1, ".fa")){
+          arg0("-fi", file1)
+          } else{
+            cli::cli_abort(
+              "{.arg file1} must be FASTA"
+            )
+          },
+        if (endsWith(file2, ".bed")|endsWith(file2, ".gff")){
+          arg0("-bed", file2)
+        } else{
+          cli::cli_abort(
+            "{.arg file2} must be BED/GFF"
+          )
+        },
+        arg0("-fo", ofile),
+      )
+    }
+  )
+)
+
+#  bedtools_closest ----
+bedtools_closest <- make_command(
+  "bedtools_closest",
+  function(
+    file1,
+    file2,
+    ofile,
+    ...,
+    `bedtools closest` = NULL
+  ){
+    assert_string(`bedtools closest`, allow_empty = FALSE, allow_null = TRUE)
+    BEDTools_Closest$new(
+      cmd = `bedtools closest`,
+      ...,
+      file1 = file1,
+      file2 = file2,
+      ofile = ofile,
+    )
+  }
+)
+
+BEDTools_Closest <- R6Class(
+  "BEDTools_Closest",
+  inherit = Command,
+  private = list(
+    alias = function() "bedtools closest",
+    setup_help_params = function() "--help",
+    setup_command_params = function(file1, file2, ofile){
+      c(
+        if (endsWith(file1, ".bed")|endsWith(file1, ".gff")|endsWith(file1, ".vcf")){
+          arg0("-a", file1)
+        } else{
+          cli::cli_abort(
+            "{.arg file1} must be BED/GFF/VCF"
+          )
+        },
+        if (endsWith(file2, ".bed")|endsWith(file2, ".gff")|endsWith(file2, ".vcf")){
+          arg0("-b", file2)
+        } else{
+          cli::cli_abort(
+            "{.arg file2} must be BED/GFF/VCF"
+          )
+        },
+        args("-D"),
+        arg0("-o", ofile),
+      )
+    }
+  )
+)

blit.Rproj

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+
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