Woes of a scientist

Not everything can be fun in the life of a scientist. For example, my work in the bioinformatics field of our laboratory makes me see a lot of annoying problems related to files, to be precise file formats. A lot of sofware in the biological sciences uses plain text files to export data to other programs (sometimes binary data, but that’s another matter). The problem comes when you have to use the output into another program. As a matter of fact, all kinds of programs use differently formatted text files, making a conversion or integration a pain. That is, unless you use some shell scripting (on Linux, obviously) to handle them. Today my editing window looked like this:

general/file-making.png

Where I was fixing by hand some text files. I should have used GNU sed and join earlier, as it would have saved loads of time, bah. With the changes (thanks, Raoul) the files made are almost perfect (one more tab than necessary but I’ll fix it tomorrow).

Also, I have to complete a couple of things for the paper we’re submitting, should be done tomorrow I hope.