SYNOPSIS

sn_helloWorld.py

Python example plugin for helping developers. Because this is an example, please see the Algorithm section below for more details.

Software requirements

None

This script is an example plugin for the basics. The steps are:

Argument parsing with argparse to conform to the required flags and positional parameter of every plugin
In main(), check on whether there are some options where we print something and exit: --help, --version, or --check-dependencies. This is done in setup(args).
If we have not exited already, move onto main(args)
Make a temporary directory to avoid collision with other instances of this script. However, the user could have also supplied --tempdir and so the script has to accept that parameter if supplied.
Make the required subfolders just in case they are not there: dir/SneakerNet/forEmail
The example analysis
1. samples = readWriteSamples(args.dir): rewrite SampleSheet.csv to dir + "/SneakerNet/forEmail/helloworld.py.tsv"
2. readWriteFlags(args.dir, args): record all parameters to the output table at dir + "/SneakerNet/forEmail/helloworld.py.tsv"
Wrap up: write all properties to the central properties table. Because other plugins write to this, the plugin appends and does not truncate.
1. writeProperties(args.dir, samples)
2. The central table for all plugins is at dir + "/SneakerNet/properties.txt"
3. Two entries are placed into properties.txt: the version and the table path.

properties.txt will be read by sn_report.pl which will email a formatted table in the plugin emailWhoever.pl.
helloworld.py.tsv will be included in the email because it is in the folder SneakerNet/forEmail. All files in that folder will be attached to the email when emailWhoever.pl runs.

This is a combined table of keys/values and samples/sampleCounter. An example table is shown below, when the script was run with --debug.