ccle

CCLE RDF converter

Get Dataset

Download data from the following web site .

• CCLE

- CCLE_DepMap_18q3_RNAseq_RPKM_20180718.gct
- CCLE_DepMap_18q3_maf_20180718.txt
- CCLE_sample_info_file_2012-10-18.txt

• Cellosaurus

- cellosaurus.txt

Check docker-compose.yaml

Edit docker-compose.yaml and build docker container using docker-compose .

docker-compose.yaml
--------------------------------
#      - [directory downloading ccle data]:/work/data/raw         for mount
#      - [RDF file output directory]:/work/output                 for mount
--------------------------------

Create docker container

docker-compose up -d

docker-compose exec ccle_cnvtr bash

Create RDF files

Edit config/prm_preprocessing.tsv

/work/
    ┣ data/
    ┃   ┗ raw/
    ┃       ┣ CCLE_RNAseq_genes_rpkm_20180929.gct
    ┃       ┣ CCLE_DepMap_18q3_maf_20180718.txt
    ┃       ┣ CCLE_sample_info_file_2012-10-18.txt
    ┃       ┗ cellosaurus.txt

Run as follow . (It takes about 30 minites / 10 core)

cd /work/scripts
python3 preprocessing.py
python3 ccle_to_rdf.py