Where you will become BFF with GFF

The average life scientist will spend a lot of time working with data. Increasingly, this data will exist in the form of large data sets that will have been downloaded or extracted from one of the many large biological databases that are accessible on the internet. Such in silico data might consist of a small number of very large files, a large number of very small files, or anything in between these extremes. However, in many cases the default file format for those files will be plain text. The actual format of the plain-text file will vary a lot, but the fact that it is plain text means there are many Unix commands that are just waiting to get their hands on your data.

This part of the book will cover a small number of extremely powerful Unix commands that are well suited for slicing and dicing text files. If you are reading this part of the book after working through the ‘Essential Perl’ section then you will spot the similarities between some of these commands and some of the operators in Perl. Conversely, if you have yet to start learning Perl, you will find this section introduces many topics that will be revisited as you learn Perl.