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chrisquince / STRONG

Strain Resolution ON Graphs
MIT License
44 stars 9 forks source link

Snakemake launcher of benchmarking scripts #42

Open snurk opened 5 years ago

snurk commented 5 years ago

Should greatly simplify regular testing on the synthetic data

Sebastien-Raguideau commented 5 years ago

I'm looking to start working on it, Chris, could you quickly point me to the scripts you usually call to do that? I'll implement it on the Test dataset first.

chrisquince commented 5 years ago

Hi Seb,

I have written a script that performs all the STRONG evaluation on the test data. It is here:

/mnt/gpfs/Hackathon/Test/CoAssembly77F/Eval.sh

It is designed to run from that dir but has environmental variables pointing to various locations. It uses a selection of scripts in:

/mnt/gpfs/Hackathon/Test/STRONG/COG_pipe/EvalScripts

and reference data from:

/mnt/gpfs/chris/Projects/NewSimulation/Select4/Test

Pleasingly on this small test strong does really well getting all strains with 99.99% accuracy!

Chris

chrisquince commented 5 years ago

I will now do a script for Desman as a comparison.