Hello ! I have a colleague who is interested in learning a scripting language to
- parse files in various formats relevant to computational biology (BAM,VCF,bed, genes lists in plain text etc,,,)
- automate processes
- do computations of course
I tried to encourage her to learn as much bash as she can but the shell has its limits. When a awk command becomes so convoluted and bloated, a little script can be helpful.
Now I am trying to think what is the best scripting language to learn for someone with no programming experience that will give her the best bang for her buck. First, a few reasons I dislike Perl
- Programming community not as active, there seems to be more libraries for the biological sciences in Python
- Can hard to read/interpret
and reasons why I dislike python:
- The @$@#( indentation system drives me insane
- Seems slower than Perl, maybe it's just in my head
- Lack of "plug and play" regular expressions
- The weird type system. I fine with the rigid C++ type system and the anything goes of Perl. But python's system can be a pain.
What are your thoughts ? Should I teach that person Perl or Python ? What is easier and better in the long run ?