Contributing

Help always wanted

AMPcombi needs your help. AMPcombi is an open-source tool developed for parsing results from published AMP prediction tools. We therefore welcome fellow contributors who would like to add new AMP prediction tools results for parsing and alignment. Whether it’s contributing patches, submitting bug reports, or just asking and answering questions on the AMPcombi repository – you are helping to make AMPcombi a better tool.

Adding a new tool

We first ask you to first make an issue on AMPcombi issues mentioning the new tool and a reference to it.

If you decide to add the code changes yourself, the next steps are:

• In the file ampcombi/reformat_tables.py:

  • add a new tool function to read the output to a pandas dataframe and return two columns labelled contig_id and prob_toolname

  • add the new function to the read_path function

• In ampcombi/ampcombi.py: add a new parameter equivalent to the new tool --<tool>_file.