Batch processing for Wormcat data
Project description
WormCat Batch
Overview
WormCat Batch is a command line tool that allows you to batch multiple runs of WormCat from a Microsoft Excel File or a directory path with WormCat formatted csv files.
Note: You can also run WormCat Batch as a docker container. Find more information on running WormCat Batch as a Docker container here.
Prerequisites
WormCat Batch requires Python 3.5+ and R 3.4.1+ with a WormCat package installed.
If you are unsure if you have WormCat installed, you can run
find.package("wormcat")
from an R command prompt.
If WormCat is not installed, you can follow the directions here to install WormCat.
Note: WormCat can be installed as an R package you; do NOT need to checkout the source unless you intend to modify WormCat. The readme file explains how to install WormCat as an R package.
Excel spreadsheet Naming Conventions
Once you have the R package installed, you will create an Excel Spreadsheet with the required data for batch execution.
See the file Example/Murphy_TS.xsl
for details on formating the Excel.
Note:
- The Spreadsheet Name should ONLY be composed of Letters, Numbers and Underscores (_) and has an extension .xlsx, .xlt, .xls
- The Sheet Names within the spreadsheet should ONLY be composed of Letters, Numbers, and Underscores (_) other characters may cause the batch process to fail!
- Each sheet requires a column name 'Sequence ID' or 'Wormbase ID' (This column name is case-sensitive)
To Run the Batch Process
To run the batch process, open a terminal window, change the directory to your project directory.
$pip install wormcat_batch
$wormcat_cli --help
After execution, the Output Directory will contain all the WormCat run data and a summary Excel spreadsheet.
Sample Output
Local development /test hints
Setup to test
- conda activate <appropriate_env>
- pip install .
Test
- cd /Users/dan/delme #some working directory
- wormcat_cli --input-excel ${PROJ_HOME}/Example/Murphy_TS.xlsx --output-path ./output
- wormcat_cli --input-csv-path ${PROJ_HOME}/Example/Murphy_TS_CSV--output-path ./output
Deploy
- Advance the version number in setup.py
conda deactivate # twine is installed in base env
increment setup.py version
cd <project directory>
rm -rf ./dist
rm -rf ./wormcat_batch.egg-info
python setup.py sdist
twine check dist/*
twine upload --repository pypi dist/*
git add .
git commit -m "some comment"
git push
Project details
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.