Basic Interactive Unix for Data Processing
Authors: Hale, Walker, Baylor College of Medicine
This talk will cover using Unix tools interactively as an alternative to downloading data files into Excel or writing one-shot custom scripts. The goal is to enable you to use combinations of standard Unix tools to accomplish more than you might think possible, especially with tabular data. I will present two motivating examples: filtering the cosmic database and joining a phenotype matrix with a genotype matrix.
The audience for this talk series consists of scientists who are not Unix developers. These are people who need to use Unix, but they are not Unix administrators nor do they write hardcore Unix-specific software. These people may aspire to write scripts in Unix or to improve the scripts they write.
- standard tools: ** awk (very basic use only) ** cat ** comm ** cut ** echo ** grep ** head ** join ** less ** sed (very basic use only) ** sort ** tr ** uniq
- redirection and pipelines (including subshells) for combining the above tools
- when to write a script