Help biologist choose a new programming language

bd spamtrap at
Fri Feb 7 05:19:47 EST 2003

Hash: SHA1

John Ladasky wrote:

> Hi, folks,
> After devoting several years to programming the most troublesome
> computers of all, namely living cells, I am beginning to take an
> interest in programming silicon again.
> Far too much has changed since I last programmed a computer.  It is
> amazing how obsolete one's knowledge can become.
> My personal programming background: 
> I need the ability to read flat-format text files, seek out some key
> words and sequence data, and analyze for patterns.  Not too difficult,
> right?

Nope. Would regexes work?

> Well, I followed one friend's advice and investigated Java, perhaps a
> little too quickly.  I purchased Ivor Horton's _Beginning_Java_2_
> book.  It is reasonably well-written.  But how many pages did I have
> to read before I got through everything I needed to know, in order to
> read and write files?  Four hundred!  I need to keep straight detailed
> information about objects, inheritance, exceptions, buffers, and
> streams, just to read data from a text file???
> I haven't actually sat down to program in Java yet.  But at first
> glance, it would seem to be a step backwards even from the procedural
> C programming that I was doing a decade ago.  I was willing to accept
> the complexity of the Windows GUI, and program with manuals open on my
> lap.  It is a lot harder for me to accept that I will need to do this
> in order to process plain old text, perhaps without even any screen
> output.
> Here is what I think would make a good programming language for me
> (but feel free to try to convince me that I should have other
> priorities):
> 1) A low barrier to entry for performing simple tasks, such as
> processing text files.  This will allow me to accomplish the job I
> want to do right now.

Perl is great for text-editing.

> 2) A language that doesn't force me to obsess about the details of
> OOP.

Perl allows OOP, but does not require it.

> 3) I would like to return to graphical applications eventually.
> Therefore the language should have a GUI library, either
> Windows-specific or cross-platform.

Once again, Perl. GTK, Tk, Qt bindings at least.

> 4) Speed is nice, but secondary.  When I consider the fact that my
> Apple II was a 1.0 MHz machine with an 8-bit data bus, and my new
> machine will be a hyper-threaded Pentium IV 2.0 GHz machine with a
> 32-bit (64-bit?) data bus, I'm willing to bet that even an Applesoft
> BASIC interpreter would be fast enough.

It's acceptably fast for me.

> Any suggestions?  (I was kidding about BASIC.)

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