[Bioperl-l] speedbumps

[Rob Edwards]

Hi all,

These are some of my thoughts on speed bumps as Nat called them (I like that term). 

Some really silly things irked me. For example sometimes the database is called GenBank, sometimes its Genbank, and sometimes its genbank (but never genBank!) This is really trivial until you are looking through a file with a case sensitive sort (like in less, my pager for perldoc). 

For SeqFeatureI.pm (and others probably) it is sometimes not clear what will be returned (scalar, array, hash). I know, I should read the pod and it will explain what is returned, but it wasn't obvious at first. Things that I thought would return a scalar returned an array (even though it only had one thing in it). However, its not clear to me how to make this more clearer as it is in the docs for most things what will be returned. Maybe a line at the start that says read the docs. There's just so much of them :)

For something like parsing genBank files, it is quite easy to call something that hasn't been defined. I realize that this is due to the haphazard nature of some genbank files, and is not easy to control for everything that may be there, but is there a way to define a set of basic fields that should be there and return a null string if they are missing from a file. At least that would stop myfirstscript.pl from throwing an error it looked for something that was missing (like organism).

In general though, I agree with Nat. There is so much there, just finding out what does what is confusing. I ended up extracting all the docs into a single file that I look through (with less) to figure out how to use something. I know there is the tutorial and whatnot, but perhaps a one line summary about each file would be another good place to start.

e.g: file xxx.pm use this to work with yyy and zzz

Now that I have written this it just seems like griping (though it is really not meant to be).

So... if others think a one line summary would be a Good Idea, I will try and put my money where my mouth is (or at least my text editor) in the next week or so and come up with something.

Rob