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 variable TAXDMP_ZIP_PATH with the path to the file.