[Bioperl-l] Syntax for load_interpro.pl?

[Hilmar Lapp]

Hi John - the load_ontology.pl script is oriented towards the end-user  
(it runs off-the-bat), indeed not the novice programmer. Was there  
something that the script doesn't do that you wanted to program into it?

	-hilmar

On Jul 5, 2009, at 11:12 PM, John LaCava wrote:

> Hi again,
>
> Thanks for the response.
>
> Actually, I felt I did not need the entire functions of the ontology  
> script, and thought I might see what
> the interpro script would generate, at the potential benefit of  
> lower complexity to me, the novice programmer.
> But I was having trouble getting the interpro script to run, since I  
> couldnt land the syntax.
>
> Anyway, I have since started writing my own script and will not  
> pursue this matter further.
>
> Best wishes,
> John
>
>
> On Jul 5, 2009, at 6:00 PM, Hilmar Lapp wrote:
>
>> Hi John,
>>
>> I presume you mean the scripts/biosql/load_interpro.pl script in  
>> Bioperl-db. It has indeed been obsoleted for a long time and I  
>> guess I should remove it because the functionality is now in  
>> load_ontology.pl. This is b/c InterPro for the purposes of BioPerl  
>> is an ontology.
>>
>> Have you found it not to work with load_ontology.pl?
>>
>> 	-hilmar
>>
>> On Jul 5, 2009, at 4:30 PM, John LaCava wrote:
>>
>>> Greetings,
>>>
>>> I am attempting to use this script, but I don't seem to be able to  
>>> determine the appropriate syntax.
>>> Documentation on this script seems minimal.  Moreover, I am not  
>>> yet terribly experienced with
>>> these endeavors.
>>>
>>> Could someone possibly provide me with an example syntax?
>>>
>>> e.g. > load_interpro.pl ...
>>>
>>> then what?
>>>
>>> I must specify -db -file -version ?
>>>
>>> I tried a couple of ways, but I get the similar errors each time:
>>>
>>> e.g.
>>> /usr/local/bin/bp_load_interpro.pl: line 29: syntax error near  
>>> unexpected token `$file,'
>>> /usr/local/bin/bp_load_interpro.pl: line 29: `my ($file, $version);'
>>>
>>> Also, from reading the comments, it appears this is supposed to be  
>>> made obsolete or superseded by
>>> the script load_ontologies.pl.  Why is this?
>>>
>>> Sorry to bother, and thanks in advance.
>>>
>>> John
>>> _______________________________________________
>>> BioSQL-l mailing list
>>> BioSQL-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/biosql-l
>>
>> -- 
>> ===========================================================
>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>> ===========================================================
>>
>>
>>
>
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-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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