# 2-PhylteR in a container

#### Damien de Vienne

#### 2023-02-27

# 1 PhylteR in a container

In addition to the R package phylter available on CRAN (https://CRAN.R-project.org/package=phylter) and on GitHub (https://github.com/damiendevienne/phylter), containerized versions of phylter (docker and singularity) are also proposed.

This may ease the use of phylter on some computing infrastructures (clusters) or for users reluctant to the R language.

The containers host python3 scrips allowing to easily run phylter with the same options than with the R package, but also perform additional tasks such as removing (pruning) outliers from input trees and/or filtering out outlier sequences from (aligned) sequence files (fasta format).

Using phylter from the container simply consists in running the `phylter.py` function, specifying various options such as the directory containing the gene trees (with -t), the job name (with -j), etc.

The containers also contain a toy dataset of 255 Carnivora genes trees and alignments from Allio et al. (2021) that will allow you to test both the correct installation of the container(s), and the use of the `phylter.py` function and its options.

## 1.1 Run PhylteR with Docker

PhylteR is available as a Docker container: https://hub.docker.com/r/treecoutheo/phylter_docker.

Here are the steps needed to use the docker version of phylter:

> Warning: you may need administrator rights to use docker!

1. Pull the latest version of phylter container from the Docker Hub repository:

    sudo docker pull treecoutheo/phylter_docker:latest

2. Run phylter on the example Carnivora dataset

    sudo docker run -v $PWD:$PWD -w $PWD treecoutheo/phylter_docker phylter.py -j Carnivora_docker -t /usr/container-data/trees

- `$PWD` specifies that you work in your local Present Working Directory. This should not be changed.
- `-j` specifies the job name for this phylter run (and thus the name of the output folder)
- `-t` specifies the folder containing the input gene trees in Newick format (one tree per file)

The command above creates the directory `Carnivora_docker` that will contain:

- `PhylteR_all_tree_named`: a single file containing all the trees with the gene ID preceding the newick.
- `phylter.out`: the phylter output file containing the log of the run and the list of identified outliers.

3. Run phylter on the example Carnivora dataset AND prune trees AND remove outliers from fasta files

You may want to run phylter and to subsequently remove the identified outliers from both the gene trees and the sequences files. For this to be performed, the sequence files must contain the same name as the corresponding tree, minus the extension if any. For example, a sequence file named `ENSG00000274286_ADRA2B_final_align_NT.aln` will be matched automatically to a tree file named `ENSG00000274286_ADRA2B.treefile`: `phylter.py` will identify the gene ID as being ENSG00000274286_ADRA2B.

    sudo docker run -v $PWD:$PWD -w $PWD treecoutheo/phylter_docker phylter.py -j Carnivora_docker -t /usr/container-data/trees -p TRUE -s /usr/container-data/alignments -g TRUE

- `-p TRUE` specifies that the input trees should be pruned by removing the outliers identified by phylter. A new directorry containing the pruned trees is created (see after).
- `-s` specifies the directory containing the sequences (see above for specifications regarding naming conventions). If this directory is specified, the input sequences will be filtered by removing the outliers identified by phylter. A new directorry containing the filtered sequences is created (see after).
- `-g TRUE` specifies that a full report (in pdf) should be produced (in addition to the default `phylter.out` file).

The command above generates, in addition to the two files described in the previous example:

- `Carnivora_docker/trees_PhylteR/`: a directory containing the trees pruned from their outliers. Note that the number of trees inside the directory can be lower than the number of trees used as input in case all species from a gene tree have been identified as outliers.

- `Carnivora_docker/seqs_PhylteR/`: a directory containing sequences with outlier sequences filtered out. The number of sequences files inside the directory can be lower than the number of sequences files used as input. Again, the number of sequence files inside the directory can be lower than the number of trees sequence files in the input directory in case all species from a gene tree have been identified as outliers.

- `report.pdf`: a PDF report containing a summary of the results.

4. Prune trees and filter out sequences AFTER the phylter run.

Instead of performing the phylter analysis and the filtering of outliers at the same time, you can do it in multiple steps. here is how, on the example dataset:

- Run phylter:

    sudo docker run -v $PWD:$PWD -w $PWD treecoutheo/phylter_docker phylter.py -j Carnivora_docker -t /usr/container-data/trees

The output file `phylter.out` will be used for performing the pruning and/or the sequence filtering (see below).

- Prune trees with `prune_tree_outliers.R`:

    sudo docker run -v $PWD:$PWD -w $PWD treecoutheo/phylter_docker prune_tree_outliers.R container-data_phylter /usr/container-data/trees Carnivora_docker/phylter.out

- Filter alignments with `remove_sequence_outliers.py`:

    sudo docker run -v $PWD:$PWD -w $PWD treecoutheo/phylter_docker remove_sequence_outliers.py -j container-data_phylter -s /usr/container-data/alignments -o Carnivora_docker/phylter.out

5. View all phylter options

`phylter.py` allows specifying all the options available in the R package. To see this list of options, simply use the `-h` option:

    sudo docker run -v $PWD:$PWD -w $PWD treecoutheo/phylter_docker phylter.py -h

## 1.2 Run PhylteR with Singularity

PhylteR is also available as a singularity container : (https://cloud.sylabs.io/library/theo.treecou/tool/phylter_singularity). Here are instructions to install (or build) and run it:

1. Pull the latest version of phylter container from the Sylabs repository:

    sudo singularity pull PhylteR.sif library://theo.treecou/tool/phylter_singularity:latest

Alternatively, you can build a singularity image from the Docker Hub repository:

    sudo singularity pull PhylteR.sif docker://treecoutheo/phylter_docker:latest

2. Run phylter on the carnivora example dataset:

    singularity exec -B $PWD PhylteR.sif phylter.py -j Carnivora_singularity -t /usr/container-data/trees

3. More options Please, refer to the description of the docker container to see how to use all the options available with the `phylter.py` function.

# 2 References

- Allio, R., Tilak, M.K., Scornavacca, C., Avenant, N.L., Kitchener, A.C., Corre, E., Nabholz, B. & Delsuc, F. (2021). High-quality carnivoran genomes from roadkill samples enable comparative species delineation in aardwolf and bat-eared fox. eLife, 10, e63167. doi: 10.7554/eLife.63167.

For comments, suggestions and bug reports, please open an issue on this GitHub repository.