Carnival_gex_preprocess

Carnival Gex Preprocess Building Block

This package provides the Carnival Gex Preprocess Building Block (BB).

Table of Contents

• Carnival Gex Preprocess Building Block
  • Table of Contents
  • Description
  • User instructions
    • Requirements
    • Installation
    • Usage
    • Uninstall
  • License
  • Contact

Description

This building block processes (reshapes and scales) gene expression data from the Genomics of Drug Sensitivity in Cancer (GDSC) database for use by other building blocks.

User instructions

Requirements

• Python >= 3.6
• Singularity
• permedcoe base package: python3 -m pip install permedcoe

In addition to the dependencies, it is necessary to generate the associated singularity image (toolset.singularity), located in the Resources folder of this repository.

They MUST be available and exported respectively in the following environment variable before its usage:

export PERMEDCOE_IMAGES="/path/to/images/"

Installation

This package provides an automatic installation script:

./install.sh

Usage

The Carnival_gex_preprocess_BB package provides a clear interface that allows it to be used with multiple workflow managers (e.g. PyCOMPSs, NextFlow and Snakemake).

It can be imported from python and invoked directly from a PyCOMPSs application, or through the command line for other workflow managers (e.g. Snakemake and NextFlow).

The command line is:

Carnival_gex_preprocess_BB -d \
    --tmpdir <working_directory> \
    --input_file <input_file> \
    --col_genes <col_genes> \
    --scale <scale> \
    --exclude_cols <exclude_cols> \
    --tsv <tsv> \
    --remove <remove> \
    --verbose <verbose> \
    --output_file <output_file>

Where the parameters are:

	Flag	Parameter	Type	Description
	--tmpdir	<working_directory>	Folder	Working directory (temporary files)
Input	--input_file	<input_file>	File	csv/url with the GDSC gene expression data
Input	--col_genes	<col_genes>	String	Name of the column containing the gene symbols. Default = GENE_SYMBOLS
Input	--scale	<scale>	String	Normalize genes across samples (TRUE/FALSE)
Input	--exclude_cols	<exclude_cols>	String	Exclude columns containing the given string. Default = GENE_title
Input	--tsv	<tsv>	String	Import as TSV instead of CSV (TRUE/FALSE)
Input	--remove	<remove>	String	Remove the given substring from columns. Default = .DATA
Input	--verbose	<verbose>	String	Verbose output (TRUE/FALSE)
Output	--output_file	<output_file>	File	Processed csv file

Here is an example from https://github.com/saezlab/permedcoe/blob/master/containers/workflow_bb.sh preprocessing GDSC data:

wget -O gdsc_gex.zip https://www.cancerrxgene.org/gdsc1000/GDSC1000_WebResources/Data/preprocessed/Cell_line_RMA_proc_basalExp.txt.zip
unzip gdsc_gex.zip
Carnival_gex_preprocess_BB \
    --input_file Cell_line_RMA_proc_basalExp.txt \
    --col_genes GENE_SYMBOLS \
    --scale FALSE \
    --exclude_cols GENE_title \
    --tsv TRUE \
    --remove DATA. \
    --verbose TRUE \
    --output_file gex.csv

Uninstall

Uninstall can be achieved by executing the following scripts:

./uninstall.sh
./clean.sh

License

Apache 2.0

Contact

https://permedcoe.eu/contact/

This software has been developed for the PerMedCoE project, funded by the European Commission (EU H2020 951773).