j-andrews7 / VAMPIRE

Variant and Epigenetic anNotation for Underlying Significance and Regulation
MIT License
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control and documented runs #29

Open Crumbs350 opened 8 years ago

Crumbs350 commented 8 years ago

configuration input file that specifies attributes/settings of run: propose: file format flat text or xml output file that documents run time/date, attributes used, output files, and primary conclusions possible format rmarkdown, json, or xml

j-andrews7 commented 8 years ago

Currently, this is all specified at the command line at the time of running. A config file isn't a bad idea, though most tools typically stick to the command line.

As for output, some of that info can and should be stuck in the output files themselves (namely the date, tool version, commands/parameters used), see activity.py, I think it sticks the date and command line options in the header of the file already. Creating a summary file with all of that info and 'primary conclusions' may still be a good idea though.

Crumbs350 commented 7 years ago

implemented venusar.py function set createConfigLookup(), read_config(), process_config() and assorted helper functions to read and process venusar_default.config or similarly formatted config files. Format defined by header of venusar_default.config and read_config() documentation. user can either use print_config() or process_config(debug=True) to test output prior to running.

These additions address original suggestion but not output comments by j-andrews7 20160930.