[Bioperl-l] Syntax for load_interpro.pl?
hlapp at gmx.net
Mon Jul 6 03:30:34 UTC 2009
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?
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,
> 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?
>> On Jul 5, 2009, at 4:30 PM, John LaCava wrote:
>>> 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:
>>> /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 made obsolete or superseded by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.
>>> BioSQL-l mailing list
>>> BioSQL-l at lists.open-bio.org
>> : 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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