Comments on: Using helper scripts to make bioinformatics analysis easier to maintain http://www.bioinformaticszen.com/2008/02/bioinformatics-helper-scripts/ Sun, 07 Sep 2008 02:56:26 +0000 http://wordpress.org/?v=2.6 By: Max http://www.bioinformaticszen.com/2008/02/bioinformatics-helper-scripts/#comment-12086 Max Mon, 03 Mar 2008 18:44:41 +0000 http://www.bioinformaticszen.com/2008/02/bioinformatics-helper-scripts/#comment-12086 Are you're talking about the use of a library for common stuff? I might have misunderstood, but is there anything more basic in programming than regrouping your common stuff in your own lib/ dir ? I guess anyone who is programming more than a couple of lines per week will use a directory with common functions he or she is using all the time, they will grow and grow by the time... Are you’re talking about the use of a library for common stuff? I might have misunderstood, but is there anything more basic in programming than regrouping your common stuff in your own lib/ dir ? I guess anyone who is programming more than a couple of lines per week will use a directory with common functions he or she is using all the time, they will grow and grow by the time…

]]> By: Chris Lasher http://www.bioinformaticszen.com/2008/02/bioinformatics-helper-scripts/#comment-12005 Chris Lasher Sun, 02 Mar 2008 23:36:54 +0000 http://www.bioinformaticszen.com/2008/02/bioinformatics-helper-scripts/#comment-12005 Andrew Hunt and Dave Thomas covered this well in The Pragmatic Programmer chapter on the "DRY (Don't Repeat Yourself) Principle". Anytime I repeat a single line of code, my Spidey-sense tingles and I think of how I can place it into a common area. Need to repeat a for-loop? Make it a function/method. Need to repeat a function/method? Put it in a module/mixin class. Need to repeat a module/class? Make a package/library. I'm not sure if you experience this, but in my experience, scripts intended as "one-offs" have a habit of staying around. Cutting and pasting between them creates crufty, brittle code. Each successive time I touch that "one-off" I make sure the code becomes more tidy when I leave it than when I open it. This way, it incrementally develops into a full-fledged module or program appropriately. And, of course, if I plan to publish the result, making sure that script has unit/functional tests is a Really Good Idea. Andrew Hunt and Dave Thomas covered this well in The Pragmatic Programmer chapter on the “DRY (Don’t Repeat Yourself) Principle”. Anytime I repeat a single line of code, my Spidey-sense tingles and I think of how I can place it into a common area. Need to repeat a for-loop? Make it a function/method. Need to repeat a function/method? Put it in a module/mixin class. Need to repeat a module/class? Make a package/library.

I’m not sure if you experience this, but in my experience, scripts intended as “one-offs” have a habit of staying around. Cutting and pasting between them creates crufty, brittle code. Each successive time I touch that “one-off” I make sure the code becomes more tidy when I leave it than when I open it. This way, it incrementally develops into a full-fledged module or program appropriately.

And, of course, if I plan to publish the result, making sure that script has unit/functional tests is a Really Good Idea.

]]>