Crate dihardts_omicstools
source ·Expand description
§Omictools
§Constant data
For easier maintenance the data of some datatypes with multiple attributes like elements and amino acids is provided as CSV-file and gets compiled on build time (see: build.rs)
- Amino acid data is used from: https://proteomicsresource.washington.edu/protocols06/masses.php
- Elements data is used from: https://proteomicsresource.washington.edu/protocols06/masses.php
- Subatomic particles data is used from en.wikipedia.org/wiki/(Proton|Electron|Neutron) (need better source)
- Krokin/Wilkins retention coefficients: https://doi.org/10.1074/mcp.M400031-MCP200
Data with one or two attributes are directly added to the code:
- Amino acid hydropathicity_kd:
Kyte, J.; Doolittle, R. F.. A simple method for displaying the hydropathic character of a protein. Journal of molecular biology 1982, 157 (1), 105-32. https://doi.org/10.1016/0022-2836(82)90515-0.
§Installation
cargo add dihardts_omicstools
§Development
§Dependencies
- Rust
- OpenSSL (Ubuntu:
libssl-dev
)
§Unit tests
- For testing the taxonomy reader a
taxdmp.zip
is required. The test is capable of download it by itself and save it to the tmp folder, however if you plan excessive testing over a couple of reboots, download it ones and set the environment variableTAXDMP_ZIP_PATH
with the path to the file.
Modules§
- Module containing functions and information for biology
- Module containing functions and information for chemistry and molecules
- Entities and functions for working with mass spectrometry data
- Module containing functions and definitions for proteomics
- Functions and extension for external crates