tongzhouxu / mashpit Goto Github PK

Need to rename master branch to perl and the python branch to master. We are moving forward with python only.

Need to add requirements for Python branch into a future README.md

This is my first attempt:

• Mash >= v2.0
• Skesa >= v2.4.0
• sratoolkit
• Python3 modules
  • Biopython
  • sqlite

Need to update database, probably the BioSample table. Need to add an outbreak code field.

Could you change it so that the results are printed to stdout instead of to a file? And if so, document it in the readme?

Could you make the database a parameter for each of the scripts? It should not always be ./mashpit.db. For example, if I had a separate database for each species, then I might have differently named databases. Or I might be in a different directory.

Need to have unit tests. Need to use standard python methods for unit tests, e.g., https://docs.python.org/3/library/unittest.html

Suggestions for your first unit tests:

• test --version and --help flags to make sure there is a desired stdout and exit code
• Creating a small (3-genome?) database
  • test metadata against expected output
  • test signatures file against expected output
  • test a dist operation against expected distance

Suggest making this into a pip-installable package with e.g., https://dzone.com/articles/executable-package-pip-install

Please create one markdown file describing how to create a test database with about 1000 samples. It should be such that any typical user can follow the instructions and that the database will come out exactly the same in my hands and in your hands and in another person's hands, etc.

Need a method so that we can run

Mashpit query Mashpit.sqlite sketch1.msh [sketch2.msh...]

Where Mashpit.sqlite is a database created by the Mashpit creation scripts and sketch1.msh is a regular mash sketch file.

Need to get outbreak examples. However, some examples do exist at https://github.com/WGS-standards-and-analysis/datasets

Need to add main documentation

• Synopsis
• Installation
• Requirements
• For the impatient -- some basic wording on how to run tests.sh

Consider using sourmash instead of system calls to mash

Just a thought for a future version (and not now) but it might be kind of awesome if we could merge two databases. If it works, it could be a mechanism for users to update local databases without having to remake them.