Adding read.treeqza to parse tree qza file from output of qiime2

DESCRIPTION

@@ -34,7 +34,8 @@ Suggests:
     testthat,
     tidyr,
     vroom,
-    xml2
+    xml2,
+    yaml
 VignetteBuilder: knitr
 ByteCompile: true
 License: Artistic-2.0

NAMESPACE

@@ -105,6 +105,7 @@ export(read.phyloxml)
 export(read.r8s)
 export(read.raxml)
 export(read.tree)
+export(read.treeqza)
 export(rename_taxa)
 export(rescale_tree)
 export(root)

R/treeqza.R

@@ -0,0 +1,34 @@
+#' @title read.treeqza
+#' @param treeqza the qiime2 output file contained tree file.
+#' @param node.label parse node label as 'label' or 'support' value.
+#' @param ... additional parameter, passed to 'read.tree'.
+#' @return phylo tree object or treedata object when node.label was parsed 'support'.
+#' @export 
+#' @examples
+#' qzafile1 <- system.file("extdata/qiime2treeqza", "fasttree-tree.qza", package="treeio")
+#' qzafile2 <- system.file("extdata/qiime2treeqza", "iqt-tree.qza", package="treeio")
+#' qzafile3 <- system.file("extdata/qiime2treeqza", "raxml-cat-tree.qza", package="treeio")
+#' tr1 <- read.treeqza(qzafile1)
+#' tr1
+#' tr2 <- read.treeqza(qzafile2)
+#' tr2
+#' tr3 <- read.treeqza(qzafile3)
+#' tr3
+#' # parse node label as 'support' value.
+#' qzafile4 <- system.file("extdata/qiime2treeqza", "raxml-cat-bootstrap-tree.qza", package="treeio")
+#' tr4 <- read.treeqza(qzafile4, node.label="support")
+#' tr4
+read.treeqza <- function(treeqza, node.label = "label", ...){
+    tmpdir <- tempdir()
+    unzipfiles <- utils::unzip(treeqza, exdir=tmpdir)
+    metadafile <- unzipfiles[grep("metadata.yaml", unzipfiles)[1]]
+    metaflag <- yaml::read_yaml(metadafile)
+    formatflag <- metaflag$format
+    if (formatflag!="NewickDirectoryFormat"){
+        stop("Please check whether treeqza file contained tree file!")
+    }else{
+        datafile <- unzipfiles[grep("data/tree.nwk", unzipfiles)]
+        x <- read.newick(datafile, node.label=node.label, ...)
+        return (x)
+    }
+}

tests/testthat/test-treeqza.R

@@ -0,0 +1,10 @@
+context("tree qza file (output of qiime2 phylogenetic inference) input")
+
+library(treeio)
+qzafile <- system.file("extdata/qiime2treeqza", "fasttree-tree.qza", package="treeio")
+
+tr <- read.treeqza(qzafile)
+
+test_that("read.treeqza should work for tree qza file",{
+    expect_true(is(tr, "phylo"))
+})