This is a rust progam written to aggregate a number of python and bash scripts which support the treeval pipeline.
Much of the code used in this package has been pulled from the FasMan.
treeval_utils [prepare_geneset | generate_csv | yaml_check] -h
The two functions are pretty much identacle, however, the first splits files by number of records in the input, the second splits by a given memory chunk (e.g. 10mb) without breaking a scaffold.
Splitbysize, is not ready for produciton, due to the time it takes to execute. This indicates an error with the algorithm.
| Args | Help |
|---|---|
| -f | input fasta file |
| -s / --memory_size | Size in megabytes that the output files should aim for |
| -d / --data_type | input is one of: "PEP", "CDNA", "CDS", "RNA", "OTHER". Keep in mind OTHER is not currently in use. |
| -c / --clean_headers | Sanitise the output files headers into a simple format |
| -r / --origin-database | Choice of ENSEMBL / NCBI / OTHER |
Take the input geneset file suplied from Ensemble or NCBI and Split it into a series of files of around $memory_size. The files will also be generated in a folder structure such as: $output-directory/[file-prefix]/$data_type/[file-prefix]-id.f{a|asta}
| Args | Help |
|---|---|
| -i / --input-directory | The top level of the geneset directory |
This function takes the top level directory where geneset data is being stored and creates a directory of csvs describing the data.
| Args | Help |
|---|---|
| -y / --input-yaml | The input yaml for TreeVal |
This function checks over a yaml for TreeVal and ensures that files can be found and that everything is usable.
## Acknowledgements
Thanks go to the Rust @ Wellcome group, Katherine Figueroa, Stephen Inglis and Dasun Pubudumal. They have helped my understanding of Rust and improved upon the original code (whilst it was in FasMs).