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

[xiangpin]

Description

Adding read.treeqza to parse tree file from output of qiime2 in phylogenetic inference step.
The tree file format is always newick format, but it is compressed as .qza file.

Related Issue

• unzip the file to temporary folder.
• checking whether the file contained .qza file is a newick format file.
• parse the file with read.newick.

Example

> library(treeio)
>
> qzafile3 <- system.file("extdata/qiime2treeqza", "raxml-cat-tree.qza", package="treeio")
>
> qzafile4 <- system.file("extdata/qiime2treeqza", "raxml-cat-bootstrap-tree.qza", package="treeio")
># parse node.label = 'label'
> tr3 <- read.treeqza(qzafile3)
> tr3

Phylogenetic tree with 20 tips and 18 internal nodes.

Tip labels:
  ed1acad8a98e8579a44370733533ad7d3fed8006, 9b220cae8d375ea38b8b481cb95949cda8722fcb, 5aba6bd9debc23ded7041ffdcfe5d68a427e8ce8, 2e3b2c075901640c4de739473f9246385430b1ed, 682e91d7e510ab134d0625234ad224f647c14eb0, d44b129a6181f052198bda3813f0802a91612441, ...

Rooted; includes branch lengths.

># parse node.label = 'support'
> tr4 <- read.treeqza(qzafile4, node.label="support")
> tr4
'treedata' S4 object'.

...@ phylo:
Phylogenetic tree with 20 tips and 18 internal nodes.

Tip labels:
  d44b129a6181f052198bda3813f0802a91612441, aa4698d2e2b1fa71d08e2934a923aad7374a18f6, 6a36152105590b1eb095b9503e8f1f226fc73e43, 418f1d469f08c99976b313028cf6d3f18f61dd55, 9b220cae8d375ea38b8b481cb95949cda8722fcb, 5aba6bd9debc23ded7041ffdcfe5d68a427e8ce8, ...

Unrooted; includes branch lengths.

with the following features available:
        'support'.

[GuangchuangYu]

it seems all the tip labels were encoded as uuid. Any idea?

[xiangpin]

Yes, qiime2 assigns version 4 universally unique identifiers (UUIDs) to each execution of an Action, and to all Results. It seems not be converted to other encoded format.

[GuangchuangYu]

any possibility to convert them back to human readable labels?

[xiangpin]

I did't find the method to solve the problem. And I found the empress also did not parse the tip labels to human readable labels.