add download_rfam_cm

Author: brendanf

NAMESPACE

@@ -4,6 +4,7 @@ export(cm_5_8S)
 export(cmalign)
 export(cmbuild)
 export(cmsearch)
+export(download_rfam_cm)
 export(read_stockholm_msa)
 export(sample_rRNA_5_8S)
 export(sample_rRNA_fasta)

NEWS.md

@@ -14,7 +14,8 @@
 * If `read_stockholm_msa()` is given an open connection, it does not close it
   when done. (But if given a filename or an unopened connection, it opens and
   then closes.)
-* `cmsearch()` correctly handles fields with spaces (e.g., description) 
+* `cmsearch()` correctly handles fields with spaces (e.g., description)
+* Add `download_rfam_cm()` to easily download RFAM covariance models.
 
 # Changes in version 0.99.4
 

R/download_rfam_cm.R

@@ -0,0 +1,26 @@
+#' Download a covariance model from RFAM
+#'
+#' @param cm (\code{character} string) the name of the CM to download. Typically
+#'     this is in the format \code{"RFxxxxx"} where the \code{"x"}'s represent
+#'     decimal digits.
+#' @param filename (\code{character} string) file to save the CM in.  The
+#'     default is to save the CM in the current working directory in a file
+#'     named \code{"RFxxxxx.cm"}.
+#' @param ... additional arguments passed on to
+#'     \code{\link[utils]{download.file}}.
+#'
+#' @return The name of the downloaded file, invisibly.
+#' @export
+#'
+download_rfam_cm <- function(cm, filename = paste0(cm, ".cm"), ...) {
+    assertthat::assert_that(
+        assertthat::is.string(cm),
+        assertthat::is.string(filename)
+    )
+    utils::download.file(
+        paste0("https://rfam.xfam.org/family/", cm, "/cm"),
+        destfile = filename,
+        ...
+    )
+    invisible(filename)
+}