Extracting relevant columns from csv files Workflow for quick look of papers from pubmed “similar or cited by” Download the citation/similar articles in csv format from pubmed Check the number of lines in the file wc -l file.csv See the names of columns of the file csvcut -n file.csv Create an output for a quick visual check with title and doi, most recent first Option 1: for the output in terminal, comma separated...
Stream editor (sed) edits text files without opening them. Most often, the editing would be a replacement of one character or word by another. This way a delimiter of a csv file can be changed from comma to semicolon, name of a person can be replaced throughout the text. But that is just a beggining; sed has much more to offer: The “word” can be a regular expression making it super flexible The lines where this replacement will be done, can be specified by their line number, range, or content Taken togehter, sed helps to delete, replace, and append characters, words, lines or whole files....
How to manage versions of documents and scripts from the command line. What is a work tree, staging, and commiting?. How can I go back to a previous version of a file? How to branch to test new variant without losing the functional version, how to tag the version. How to push to GitHub from the command mode using ssh authorization. Resource ProGit book link first three chapters are sufficient....
Command line utility ffmpeg, dedicated to different transformations of video, is one of the tools which genuinly feel like magic. I do not work with video on day to day basis, and when I do, there usually is a deadline looming. What happens when there is a deadline? I realize couple of things at the last minute: Different format of the video is required. Video is too big and my institutional mail will not cope with this size of attachment....