Reproducibility test

Testing InstaNexus reproducibility

conda environment in linux uses python version 9 conda environment in osx uses python version 11

First check: check conda environment

Running script_dbg.py and script_greedy.py scripts that use all the packages required in the folder src

1. Any problems with any packages? ✅
2. Can you run the scripts with no breaks? ✅

Note: at the moment some problems appear in the terminal probably related to the library kaleido for saving images.

• problem solved: kaleido version 0.2.1 is required or it needs google chrome browser to be installed to show/write images

Second check: script_dbg.py and script_greedy.py scripts

Consider a specific combination of values for a specific dataset (it is already specified in the script)

1. Do we obtain the same statistical results? check inside folder output the folder "statistic" - json file scaffold
   • dbg ✅
   • greedy ✅
2. Do we obtain the same number of outputs? check inside folder output the folder "scaffold": example cluster fasta
   • dbg ✅
   • greedy ✅
3. Check few scaffolds and see if the sequence is the same
   • dbg ✅
   • greedy ✅

Third check: check grid search optimization

Considering specific samples and combinations, check the tables if release same results

1. gridseach.py on greedy ? ❌
2. gridsearch.py on DBG ? ❌