![]() If you’d rather add the output of your commands to an existing file, you can use > instead.įor example, the following command (which will be described in more detail in the first recipe) will print all of the lines of the file input.csv that do not begin with a # character: If that file exists, > will replace its contents with the new output. If the output file doesn’t already exist, > will create that file. To do this, just add the > character and the name of the file where you want the output to be stored to the end of the command. With output redirection, you can tell the command line to write the output of one or more commands to a file instead of printing it to the screen. This might be ok when doing some calculations, but it’s not so useful if you’re transforming files (like CSVs) and intend to save them, share them, or use the results in some other software. Writing Output to a File with Output Redirectionīy default, most command line tools give their results by printing them to the screen. By knowing just a handful of commands, just about anything is possible. ![]() The real power of the command line comes from stringing these programs together to perform more complex tasks. Most of the commands available on the command line were developed with the same goals: to do a single job and to do it well. A Quick Introduction to Pipes and Redirection Most software that handles CSVs isn’t picky, and allows you to specify the delimiter used. Just replace the comma character in the commands with your delimiter of choice. Although you can read it from start to finish (it’s not that long), each “recipe” is a self-contained guide for doing a particular task with a CSV file.Īlthough we’re focusing on comma-separated values, all of the commands below would work for data separated by tabs or any other separator. This guide is intended to be used like a cookbook. If you’re already familiar with these, you can jump right into the good stuff. In the next section, I’ll quickly introduce two of the command line’s most powerful features: pipes and output redirection. I’ve also included a brief description of the command line tools used in this cookbook below in A Quick Overview of the Commands Used in this Cookbook. If these topics are new to you, there’s a pretty good introduction linked below in Some Useful Resources. You don’t have to be a command line wizard to use the commands below, but you do need to know the basics of how to get to a command line (hint for OS X users, it’s through the Terminal app) and how to do things like changing directories ( cd) and listing files ( ls). Even though the Unix command line has existed for decades, it’s still always just a few clicks away, whether you use Linux on some HPC hardware or cloud service, or whether you use Mac OS X on your laptop. This power, speed, and flexibility extends to working with CSV files, and it’s here that I’d like to demonstrate a small slice of what can be done with just a few keystrokes. Those familiar with working in the command line, however, wouldn’t trade its power, speed, and flexibility for anything, no matter how shiny or “user friendly” an alternative drag-and-drop interface might be. To many, the command line (or shell) is a strange and scary place. Support for CSV files is built into most data analysis software, programming languages, and online services (see Some Useful Resources at the end of this article for links for your software of choice). CSVs are also version-independent, so ten years down the road you won’t have to track down some ancient piece of software in order to revisit your data (or do the same for someone else’s data). Because they are plain text, these files can be easily read and edited without the need for specialized or proprietary software. ![]() This format offers several significant advantages. Within the file, each row contains a record, and each field in that record is separated by a comma, tab, or some other character. CSV is an informally-defined file format that stores tabular data (think spreadsheets) in plain text. Working with CSVs on the Command Line September 23, 2013Ĭomma-separated values (CSV), and its close relatives (e.g., Tab-separated values) play a very important role in open access science.
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