Re: Syntax for load_interpro.pl?
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Re: Syntax for load_interpro.pl?
by John LaCava
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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 made obsolete or superseded by 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@... >> http://lists.open-bio.org/mailman/listinfo/biosql-l > > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : > =========================================================== > > > _______________________________________________ Bioperl-l mailing list Bioperl-l@... http://lists.open-bio.org/mailman/listinfo/bioperl-l |
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Re: Syntax for load_interpro.pl?
by Hilmar Lapp
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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@... >>> http://lists.open-bio.org/mailman/listinfo/biosql-l >> >> -- >> =========================================================== >> : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : >> =========================================================== >> >> >> > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@... > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== _______________________________________________ Bioperl-l mailing list Bioperl-l@... http://lists.open-bio.org/mailman/listinfo/bioperl-l |
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Re: Syntax for load_interpro.pl?
by John LaCava
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Hi again,
No, mainly I was scanning the different scripts to see if any of them were friendly towards capturing the InterPro domain-type info that we discussed in relation to load-seqdatabase.pl. I plan to explore the options you mentioned in your other reply to that thread, so that I can take full advantage of this script and the BioSQL schema... However, in the mean time I have authored a small and somewhat crappy script that will capture the SwissProt protein ID and accession number as well as the InterPro accession number and domain type and pass these into the bioentry and dbxref tables of the BioSQL schema. I had to add an additional column to the dbxref table that would accept the InterPro domain type (the optional ID) since I couldn't get it into dbxref_qualifier_value table without upsetting the mysql foreign key settings. Cheers again, John On Jul 5, 2009, at 11:30 PM, Hilmar Lapp wrote: > 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@... >>>> http://lists.open-bio.org/mailman/listinfo/biosql-l >>> >>> -- >>> =========================================================== >>> : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : >>> =========================================================== >>> >>> >>> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l@... >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : > =========================================================== > > > _______________________________________________ Bioperl-l mailing list Bioperl-l@... http://lists.open-bio.org/mailman/listinfo/bioperl-l |
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