USAGE:
perplexity eval [OPTIONS] --output <output> --quants <train_ecs> --test_ecs <test_salmon_dir> --train_ecs <train_ecs>
FLAGS:
-h, --help Prints help information
-V, --version Prints version information
OPTIONS:
-o, --output <output> Write results to output
--quants <train_ecs> Training set quant.sf
--smoothing <smoothing> Smoothing parameter for various strategies [default: 1e-8]
-m, --smoothing_strategy <mode> One of {TX, TPM, LGT} [default: LGT]
--test_ecs <test_salmon_dir> Test set equivalence class file
--train_ecs <train_ecs> Training set equivalence class file
Use perplexity --help for more options
See snakefiles/config.yml for details regarding input filepaths and conventions for setting up k-fold quantify-then-validate procedure. Supplied perplexity.snk snakefile runs Salmon on k-folds then computes perplexity of held-out reads on quantified reads. kfold.snk is used to set up quantify-validate fragment sets.
snakemake --snakefile snakefiles/perplexity.snk --configfile <config file> -j <n jobs>
snakemake --snakefile snakefiles/kfold.snk --configfile <config file> -j <n jobs>
cargo build --release