[Biojava-dev] Hi.. Calling Java from Perl

[Andy Yates]

Hi Abhi,

Well to answer your first question the only real way to do this is by  
shelling out to Java. Inter-process communication could then be dealt  
with by writing to temporary files or maybe communicating back over  
STDOUT.

The question I would ask you though is what particular part of BioJava  
are you using? Is there any reason why another similarly named Bio  
project (shall not mention it here as I think people think I'm  
becoming weak when it comes to Perl) cannot be used? As always when  
programming avoiding shelling out to another program if possible is  
always a good idea; sometimes it cannot happen say if you want to run  
clustalw but say shelling out to delete a file is unnecessary.

Andy

On 28 Jul 2009, at 20:04, Abhishek Pratap wrote:

> Hi Guys
>
> Before I ask the question, let me introduce myself. I am Abhishek
> primarily a Bioinformatician and this is my first mail here. I
> realized sooner thn later that I have to use BioJava to make my life
> easier. :)
>
> So basically we have a lot of perl code where we would like to plugin
> some Biojava code and some inhouse written packages/classes. I am just
> wondering what is the best way to do so. Clearly I am not a java guy
> so please excuse me in case I am asking something which is very basic.
> I found couple of solutions after few googles but not sure which is
> the efficient one.
>
> Thanks,
> -Abhi
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev