bromberglab/funtrp repository overview

⁠fuNTRp - function Neutral/Toggle/Rheostat predictor

A Random Forest-based predictor to classify protein positions by type based on the expected range of mutational impacts at that position: Neutral (most mutations have no or weak effects), Rheostat (range of effects; i.e. func-tional tuning), or Toggle (mostly strong effects).

⁠Requirements

• Docker (https://www.docker.com⁠)
• Sequence database (RostLab Big_80 database, size: 27.27 GB; http://www.rostlab.org/services/ppmi/download_file?format=gzip&file_to_download=db⁠); A Docker image of PredictProtein (bromberglab/predictprotein) will be downloaded automatically.

⁠Usage

⁠1 Get sources

Open a terminal and checkout the funtrp repository:

git clone https://[email protected]/bromberglab/funtrp.git

or download the zipped version:

curl --remote-name https://bitbucket.org/bromberglab/funtrp/get/master.zip
unzip master.zip

The following steps assume the current working directory as the funtrp (repository) base directory.

⁠2 Sequence Database

Download and extract the sequence database⁠. Move files located in data/big/ and starting with big_80 into the db/ folder of the funtrp base directory; any other databases in the data/ directory are not required and can be deleted. Open a terminal, navigate to the funtrp base directory and execute:

cd db/
wget -O rostlab-data.txz "http://www.rostlab.org/services/ppmi/download_file?format=gzip&file_to_download=db"
xz -d rostlab-data.txz
tar xvf rostlab-data.tar
mv data/big/big_80* .
rm -rf data rostlab-data.tar

⁠3 Docker image

Docker images are available via the Docker cloud or can be build from the sources available in this repository.

⁠3.1 Use available docker images

Open a terminal and execute:

docker pull bromberglab/predictprotein
docker pull bromberglab/funtrp

⁠3.2 Build funtrp docker image from sources

Open a terminal, navigate to the funtrp base directory and execute:

docker build -t bromberglab/funtrp .

⁠4 Run funtrp

funtrp can be run using the provided binary (funtrp.sh in the base directory) or directly via the docker engine.

⁠4.1 Run funtrp using available binary

Open a terminal and execute:

<ABSOLUTE_PATH_TO_FUNTRP_BASE>/funtrp.sh <PATH_TO_QUERY_FASTA_FILE>

⁠4.2 Run funtrp using docker engine directly

Copy a query sequence in fasta format (<QUERY_ID>.fa or <QUERY_ID>.fasta)to the mnt/ folder in the funtrp base directory (note here, that <QUERY_FILE_NAME> refers to the filename without any path information and <QUERY_ID> refers to the query file name without extension). Then open a terminal, navigate to the funtrp base directory and execute:

docker run --rm \
        -v <ABSOLUTE_PATH_TO_FUNTRP_BASE>/db:/usr/share/rostlab-data/data/big \
        -v <ABSOLUTE_PATH_TO_FUNTRP_BASE>/mnt:/mnt/local-storage \
        bromberglab/predictprotein predictprotein \
        --target=query.profRdb --target=query.mdisorder --target=consurf \
        --output-dir=/mnt/local-storage/pprotein/<QUERY_ID> --work-dir=/mnt/local-storage/pprotein/<QUERY_ID>/tmp \
        --seqfile=/mnt/local-storage/<QUERY_FILE_NAME> \
        --num-cpus=2 \
        --blast-processors=10

docker run --rm \
        -v <ABSOLUTE_PATH_TO_FUNTRP_BASE>/db:/rheostat/db \
        -v <ABSOLUTE_PATH_TO_FUNTRP_BASE>/mnt:/mnt bromberglab/funtrp <QUERY_FILE_NAME>

⁠5 Example

Open a terminal, navigate to the funtrp base directory and execute:

./funtrp.sh example/P37173.fasta

Results will then be available at mnt/P37173_funtrp.csv