maragkakislab/nanoplen

Improve documentation and code structure

mnsmar opened this issue · 6 comments

mnsmar commented

In README.md:

  • Step by step instructions for how to use the helper python tools.
  • Test datasets with step by step processing commands to use nanoplen.
  • Expand description of the output file.
  • Polish the text.

For code:

  • #22
  • #23
  • Remove travis.
  • Remove sam_per_ref_count_statistics.py cause it's not part of the nanoplen pipeline.
  • Prepare yaml file for suggested conda environment.
  • Add a descriptive header in the R script.
  • Add helper python scripts that can create simple plots following diff_length.R execution. Add example images in README.md for the example data.
  • Delete existing code in tests/ and replace with unit tests for the R code.
leetaiyi commented

Removed travis

leetaiyi commented

sam_per_ref_count_statistics.py removed

leetaiyi commented

Unit test framework and many unit tests made. Can add additional at any time.

leetaiyi commented

R scripts documented but needs proofreading

leetaiyi commented

Left "Polish the text" unchecked until more proofreading done