At What You're Doing Is Rather Desperate, Neil Saunders gives a crash course on the basics of parsing bioinformatics files. Some of his steps along the way include, first and foremost, searching for an existing parser; then visualizing the desired output, mastering regular expressions (in your chosen language), and imagining the exceptions ("Here, I raise my hand to admit that this is an area in which I need to improve," Saunders says).

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