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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.
- Requirments for running PRONTO locally
- Repository contents
- Run PRONTO locally
- Example commands
- PRONTO Docker
- PRONTO Singularity
- ChangeLog
- This tool needs to be run with python above version 3.
- Module xlutils and pptx need to be installed for python:
-
To install module xlutils, run the command:
sudo pip3 install xlutils
-
To install module python-pptx, run the command:
sudo pip3 install python-pptx
-
- Module xlrd and xlwt are needed for MTF importing function:
-
Download the files from Internet. Please google search it and choose the correct version for your environment.
-
Under the downloaded folder and install the module with command:
sudo python setup.py install
-
INPUT file name: | Details: |
---|---|
Script/PRONTO.py |
The executable python script. |
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. |
- In
Config/configure_PRONTO.ini
, please specify your InPreD node by defining value of theinpred_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 thedata_path
parameter.
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.
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
python3 Script/PRONTO.py -h
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.
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.
docker pull inpred/pronto:latest
- Specify your InPreD node name as the value of the
inpred_node
parameter in theConfig/configure_PRONTO.ini
file. - Keep the
data_path
parameter's value set to/pronto/tsoppi_data/
in the same config file.
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.
singularity pull PRONTO_singularity_image.sif docker://inpred/pronto:latest
- Specify your InPreD node name as the value of the
inpred_node
parameter in theConfig/configure_PRONTO.ini
file. - Keep the
data_path
parameter's value set to/pronto/tsoppi_data/
in the same config file.
singularity exec \
--no-home \
-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.
- First tracked version.