![]() The grep command is used to search a file for a given word or pattern and print any line containing the word/pattern. ![]() However, most of them should be pretty consistent across different Linux distributions and OS X, which are the OSs used by the vast majority of scientists that need to do any appreciable amount of programming or data processing. ![]() I understand that Linux ≠ UNIX, so it’s possible that not all of the details I discuss here will be portable across all UNIX distributions. So here is the first installment of my exploration into UNIX commands that I thought I already knew how to use! □Ī quick note: I primarily used the Fedora Linux CLI and man pages for this exercise. I decided that taking the time to really familiarize myself with 10-20 of the most common UNIX commands will in the long run save me time and make me a better, more efficient biologist. In a recent post, I lamented about the fact that I’ve been using Perl one-liners to do a simple task I could have been using a UNIX command for all this time. This makes it even easier to leverage powerful command line tools that UNIX offers.ĭespite the experience I have gained, I know there is a lot more worth learning. Also, since so many of my data processing tasks were one-off jobs, I started replacing my scripts with short little in-line programs that I wrote and executed all in a single shell command. As I gained more experience with programming and with UNIX shell commands, my scripts become shorter, more concise, and more efficient, and I began to pipe these together with shell commands on a regular basis. When I was first cutting my bioinformatics teeth, I would typically approach data processing tasks by writing a dedicated script or program. There is only so much you can do with Excel, so basic programming skills and familiarity with the UNIX command line are becoming increasingly essential to biologists. We are in an age where success in biology is eventually going to require some data processing.
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