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So we've covered a number of "framework" topics – argument handling, stream handling, error handling – in a systematic way. This section presents various tips and tricks for actually manipulating data, which can be useful both in writing scripts and in command line manipulations.
For datasome of the discussions below, we'll use a couple of data files from the GSAF's (Genome Sequencing and Analysis Facility) automated processing to deliver that delivers sequencing data to customers. These files have information about GSAF's sequencing runs (a machine run, with many customer jobs), sequencing jobs (representing a set of customer samples), and samples (a library of DNA molecules to sequence on the machine).
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perl pattern matching
If grep pattern matching isn't behaving the way I expect, I turn to perl. Here's how to invoke regex pattern matching from a command line using perl:
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