PRONTO

(rePort geneRator fOr iNpred Tumor bOards)

PRONTO is a tool used to filter and analyse data from TSO500 analysis (in the form of TSOPPI results). It generates powerpoint patient reports using predefined powerpoint template file. This repository contains the config file, metadata files, executable script, report template, testing data, and docker files to run this tool locally or in Docker/Singularity. The repository is accompanied with a docker image that is automatically pushed to dockerhub on each version release.

Table of contents

1. Requirments for running PRONTO locally
2. Repository contents
3. Run PRONTO locally
4. Example commands
5. PRONTO Docker
6. PRONTO Singularity
7. ChangeLog

Requirments for running PRONTO locally

1. This tool needs to be run with python above version 3.

2. Install required modules with the requirements.txt file:

   sudo pip install -r requirements.txt
   

Repository contents

INPUT file name:	Details:
Script/PRONTO.py	The executable python script.
pronto/pronto.py	PRONTO module containing auxiliary functions
Config/configure_PRONTO.ini	The configure file. Needs to be modified prior to its first use.
In/Templates/MTB_template.pptx	The template file used for generating PP report. (TODO: explain PP)
In/InPreD_PRONTO_metadata.txt	The clinical data file. Reports will be generated for the Sample_id for which the Create_report value is set to Y in this file.
In/MTF/IPD-XXXX_Material Transit Form InPreD NGS.xlsx	The material file contains all patient personal information. (Used by OUS) This file will generate the inpred-samle-id following the nomenclature file.

OUTPUT file/folder name:	Details:
Out/$runID/IPZXXXX	The folder contains all results for sample IPZXXXX from sequencing run $runID.
Out/$runID/IPZXXXX/extra_files	The folder contains filter tables during the calculation process, and the patient material file from lab.
Out/$runID/IPZXXXX/IPZXXXX_MTB_report.pptx	The PP report file. (TODO: explain PP)
Out/$runID/IPZXXXX/IPZXXXX_Remisse_draft.docx	The remise draft file for email. (Used by OUS)
Out/InPreD_PRONTO_metadata_tsoppi.txt	The file contains clinical data and the TSOPPI results for all sample reports.

Files located in the Testing_data folder :	Details:
testRunID="191206_NB501498_0174_AHWCNMBGXC"	testRunID is used in the following lines of this table as a shortcut for the full ID of the sequencing run, which is 191206_NB501498_0174_AHWCNMBGXC.
$testRunID_TSO_500_LocalApp_postprocessing_results.zip	The testing data from AcroMetrix sample TSOPPI results which only contains the files PRONTO needs. Move this folder into your local TSOPPI result path for testing.
InPreD_PRONTO_metadata.txt	The file contains clinical data of AcroMetrix samples for testing. Move this file into In folder of this repository for testing.
$testRunID.zip	The testing results from AcroMetrix sample TSOPPI results for your local comparisons.

Run PRONTO locally

Adapt the config file:

• In Config/configure_PRONTO.ini, please specify your InPreD node by defining value of the inpred_node parameter. The node name will appear in the header of the reports.
• In Config/configure_PRONTO.ini, please specify the local dataset file path of TSOPPI results by defining value of the data_path parameter.

Type clinical data into the input metadata file:

Manually write the clinical data into file In/InPreD_PRONTO_metadata.txt. Reports will be generated for the Sample_id for which the Create_report value is set to Y in this file.

Load local pronto module:

Load pronto module into local env to allow python to find it:

export PYTHONPATH=$PYTHONPATH:$local_pronto_path/pronto/

Run PRONTO:

PRONTO takes in TSOPPI data, clinical info provided in In/InPreD_PRONTO_metadata.txt, and powerpoint template In/Templates/MTB_template.pptx. It generates a patient report for every Sample_id with the Create_report set to Y in the Out folder and updates the file Out/InPreD_PRONTO_metadata_tsoppi.txt with the TSOPPI results of the patients for which the reports were generated.

To print the usage information run the following command:

python3 Script/PRONTO.py --help

To execute the command and generate the reports as defined in the input metadata file, run the command:

python3 Script/PRONTO.py 

Example commands

Print the usage information:

python3 Script/PRONTO.py -h

Execute the report generating process:

python3 Script/PRONTO.py

After executing the script and generating all the required reports, update the Create_report value to N for every sample for which the report should not be re-generated in the future.

Special commands used by OUS:

python3 Script/PRONTO.py -r <TSO500_runID> -D <DNA_sampleID> -c
python3 Script/PRONTO.py -m

• -c, --clinical_file: Fill the patient personal information into file InPreD_PRONTO_metadata.txt with the MTF files under the foder In/MTF/.
• -m, --mail_draft: Generate the Remisse_draft.docx file with report.

PRONTO Docker

Download the image with the latest tag:

docker pull inpred/pronto:latest

Modify content of the config file:

• Specify your InPreD node name as the value of the inpred_node parameter in the Config/configure_PRONTO.ini file.
• Keep the data_path parameter's value set to /pronto/tsoppi_data/ in the same config file.

Run PRONTO with docker image:

sudo docker run \
	--rm -it \
	-v $tsoppi_data:/pronto/tsoppi_data \
	-v $InPreD_PRONTO_metadata_file:/pronto/In/InPreD_PRONTO_metadata.txt \
	-v $pronto_output_dir:/pronto/Out \
	inpred/pronto:latest \
	python /pronto/Script/PRONTO.py

• $tsoppi_data is the path of your local TSOPPI results, which contains all runs of TSOPPI data (not the folder for individual runs).
• $InPreD_PRONTO_metadata_file is your local InPreD meta data file which contains clinical data for the samples.
• $pronto_output_dir is the path in your local environment to store the reports generated by PRONTO.

PRONTO Singularity

Download PRONTO singularity image with the latest tag:

singularity pull PRONTO_singularity_image.sif docker://inpred/pronto:latest

Modify content of the config file:

• Specify your InPreD node name as the value of the inpred_node parameter in the Config/configure_PRONTO.ini file.
• Keep the data_path parameter's value set to /pronto/tsoppi_data/ in the same config file.

Run PRONTO image with Singularity:

singularity exec \
	--no-home \
	-B $config_file:/pronto/Config/configure_PRONTO.ini \
	-B $tsoppi_data:/pronto/tsoppi_data \
	-B $InPreD_PRONTO_metadata_file:/pronto/In/InPreD_PRONTO_metadata.txt \
	-B $pronto_output_dir:/pronto/Out \
	-W $SINGULARITY_TMP \
	$dir/PRONTO_singularity_image.sif \
	python /pronto/Script/PRONTO.py

• $tsoppi_data is the path of your local TSOPPI results, which contains all runs of TSOPPI data (not the folder for individual runs).
• $InPreD_PRONTO_metadata_file is your local InPreD meta data file which contains clinical data for the samples.
• $pronto_output_dir is the path in your local environment to store the reports generated by PRONTO.py.

ChangeLog

v2.1.2

• New Features: #68
• Resolved Isses: #71 #72

v2.0.1

• New Features: (TODO: fill in)
• Resolved Isses: Bug fix reported from OUS (https://github.com/InPreD/PRONTO/commit/e34fe6a70d20c60503207ddd13319950312dd02b)

v2.0.0

• New Features: #53 #55 #56 #60 #61
• Resolved Issues: #48 #50 #63 #67

v1.3.0

• New Features: Developed by Martin.
• Resolved Issues: (TODO: fill in)

v1.2.0

• New Features: (TODO: fill in)
• Resolved Issues: Fixed the bug of RNA_material_id, problem reported in the "Issues", update all the script fitting for the new MTF format version 2024.

v1.1

• New Features: (TODO: fill in)
• Resolved Issues: #5 #7 #8 #14 #17
• Other Changes: (TODO: fill in)

v1.0

• First tracked version.