Fourth version

[anamika-yadav99]

Addresses issue #30 and issue #32

[manulera]

Hi Anamika,

I haven't had a look at the code yet, but you should invest more time in the documentation. Your readme does not address the points that I raised in our previous email exchange:

You should explain what your pipeline does so that someone that comes to the repo for the first time understands it. This should cover:

• How/where are allele features defined.
  • What do the output files look like, with some examples, e.g. take an example genotype and explain how the output in each file will be. Not addressed
  • How to download the fluorescent protein data (this could go in the readme section Getting the data). Not addressed
• Also, the issue mentioned that there should be:
  • Step-by-step guide on how to run the pipeline, taking the public available strains in nbrp_strains. Should be improved
  • Instructions to write your own format.py, with some example. Should be improved

You should start the documentation of the pipeline by briefly explaining:

• What is the starting data (lists of genotypes)
• What information we want to extract from them
• What is the extra input files that we use and what do they contain (what types of allele features, how they are defined in the toml files)
• What does the output of a particular example line in strains.tsv look in:
  • All the output files of build nltk_tags
  • All the output files of summary_nltg_tags

Some other things I noticed so far:

• summary_nltg_tags should be renamed to summary_nltk_tags
• The tests should be improved. When testing, you should use a shorter test_strains.tsv, but verify that all generated files are correct, the ones produced by build_nltk_tags and summary_ntlk tags.