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

[Abhishek Pratap]

Hi Andy

Thanks for a quick reply.  I think SHELLING out will be too process
intensive as we expect thousands of call to same Java method. I also
read about the Perl modules Java::Inline. Is that any good ?

And to answer your second question I am basically using a inhouse
method which in turns used a lot of BioJava classes for DNA
manipulation.

Thanks,
-Abhi

On Tue, Jul 28, 2009 at 5:54 PM, Andy Yates<ayates at ebi.ac.uk> wrote:
> 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
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>
>