Re: [Gusdev-gusdev] Re: LoadPfam doubts

[Chris S. <sto...@pc...>]

Hi Sucheta,
I'm guessing that they would be in DoTS.AAFeatureImp table either in  
the PredictedAAFeature or DomainFeature views as both have FKs from  
PfamEntry.
Chris

On Dec 24, 2003, at 8:23 AM, Sucheta Tripathy wrote:

> Hi Terry,
>
> Thanks for the reply.
> I wanted to know where the sequence alignments are stored in GUS. I
> presume the loadpfam uploads data into sres.dbref, dots.dbrefpfamentry  
> and
> dots.pfamentry. But none of these tables seem to have the alignement  
> data.
>
> Any comments.
>
> Sucheta
>
>> Sucheta,
>> I'm not sure what sequence alignment you mean, maybe
>> those coming from the Pfam files.
>> This is what I used
>>   ga +run GUS::Common::Plugin::LoadPfam
>> --flat_file=/home/gus/pfam/Pfam-A.full --release=9.0 --commit
>> where Pfam-A.full comes from the Pfam website.
>>
>> The attached log file might be of use.
>>
>> Terry
>>
>>
>> On  0, sucheta Tripathy <su...@vb...> wrote:
>>> Hi,
>>>
>>> I was using Loadpfam module and could not detect where the sequence
>>> alignment goes.
>>>
>>> Can anyone answer this.
>>>
>>> Thanks
>>>
>>> Sucheta
>>>
>>>> Paul, I see what you mean. Thanks for taking
>>>> time out to shed light on this.
>>>>
>>>> Happy holidays,
>>>>
>>>> Terry
>>>>
>>>> On  0, Pjm <pj...@sa...> wrote:
>>>>> Hi Chetna, Terry,
>>>>>
>>>>> I dunno if this has already been answered. Apologies if so.
>>>>>
>>>>> The Pfam-A.full file I used has duplicate entries which is quite
>>> normal.
>>>>> In
>>>>> this cut down example you can see two database references to the  
>>>>> same
>>>>> protein but the numbers following it are different;
>>>>>
>>>>> 	# STOCKHOLM 1.0
>>>>> 	#=GF ID   Acyl_CoA_thio
>>>>> 	.
>>>>> 	.
>>>>> 	#=GF DR   PDB; 1c8u A; 147; 281;
>>>>> 	#=GF DR   PDB; 1c8u B; 147; 281;
>>>>> 	#=GF DR   PDB; 1c8u A; 17; 115;
>>>>> 	#=GF DR   PDB; 1c8u B; 17; 115;
>>>>>
>>>>> The numbers are the co-ords on the protein that match up to  
>>>>> PF02551.
>>>>> Because the code tries to create another DoTS.DbRefPfamEntry for  
>>>>> both
>>> of
>>>>> these entries it gives a warning for each.
>>>>>
>>>>> 	Duplicate reference to db_ref_id 1351 from pfam_entry_id 91
>>>>> 	Duplicate reference to db_ref_id 1352 from pfam_entry_id 91
>>>>>
>>>>> Does this help?
>>>>> Paul.
>>>>>
>>>>> Chetna Warade wrote:
>>>>>> Hello Terry,
>>>>>>
>>>>>> Thanks for the log. I am looking at it and observed
>>>>>> that the pfam_entry_id in your log is a continous
>>>>>> number from the log whereas for me its different.
>>>>>>
>>>>>> Thanks again,
>>>>>> Chetna
>>>>>>
>>>>>> --- Terry Clark <tw...@cs...> wrote:
>>>>>>
>>>>>>> Hi, Chetna,
>>>>>>> I also experienced numerous duplicate entries in the
>>>>>>> pfam load.
>>>>>>> I assumed these were problems with Pfam
>>>>>>> organization, and not
>>>>>>> being a priority to me, I did not track them down;
>>>>>>> but I have
>>>>>>> a not in my log to do so. I've attached my Pfam load
>>>>>>> output
>>>>>>> for comparison.
>>>>>>>
>>>>>>> Terry
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On  0, Chetna Warade <wa...@ya...> wrote:
>>>>>>>
>>>>>>>> Hello Debbie,
>>>>>>>>
>>>>>>>> I am loading (commit) Pfam data  in GUS from
>>>>>>>
>>>>>>> scratch.
>>>>>>>
>>>>>>>> I am getting few duplicate errors e.g.
>>>>>>>>
>>>>>>>> Duplicate reference to db_ref_id 621 from
>>>>>>>> pfam_entry_id 1073
>>>>>>>>
>>>>>>>> Is this behavior okey? If not do you have any idea
>>>>>>>> about  fixes for this.
>>>>>>>>
>>>>>>>> Thanks in advance,
>>>>>>>> Chetna
>>>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> __________________________________
>>>>>> Do you Yahoo!?
>>>>>> New Yahoo! Photos - easier uploading and sharing.
>>>>>> http://photos.yahoo.com/
>>>>>>
>>>>>>
>>>>>> -------------------------------------------------------
>>>>>> This SF.net email is sponsored by: SF.net Giveback Program.
>>>>>> Does SourceForge.net help you be more productive?  Does it
>>>>>> help you create better code?  SHARE THE LOVE, and help us help
>>>>>> YOU!  Click Here: http://sourceforge.net/donate/
>>>>>> _______________________________________________
>>>>>> Gusdev-gusdev mailing list
>>>>>> Gus...@li...
>>>>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> -------------------------------------------------------
>>>>> This SF.net email is sponsored by: SF.net Giveback Program.
>>>>> Does SourceForge.net help you be more productive?  Does it
>>>>> help you create better code?  SHARE THE LOVE, and help us help
>>>>> YOU!  Click Here: http://sourceforge.net/donate/
>>>>> _______________________________________________
>>>>> Gusdev-gusdev mailing list
>>>>> Gus...@li...
>>>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>>
>>>>
>>>> -------------------------------------------------------
>>>> This SF.net email is sponsored by: IBM Linux Tutorials.
>>>> Become an expert in LINUX or just sharpen your skills.  Sign up for
>>> IBM's
>>>> Free Linux Tutorials.  Learn everything from the bash shell to sys
>>> admin.
>>>> Click now! http://ads.osdn.com/?ad_id=1278&alloc_id=3371&op=click
>>>> _______________________________________________
>>>> Gusdev-gusdev mailing list
>>>> Gus...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>>
>>>
>>>
>>> --
>>> Sucheta Tripathy
>>> Virginia Bioinformatics Institute
>>> 1880 pratt drive,Bldg XV
>>> Virginia tech.
>>> Blacksburg
>>> Virginia
>>> VA 24061
>>> phone-(540)231-8138
>>
>>
>> ********************************************************************** 
>> ****
>>
>>
>>
>> Terry Clark, July 9, 2003
>>
>> Download Pfam-A.full from Pfam website, or check on amrit at  
>> ~gus/pfam.
>> Register GUS::Common::Plugin::LoadPfam plugin.
>>
>> Load database references used by Pfam. These only need
>> to be in the sres.externaldatabase and sres.externaldatabaserelease
>> tables.
>>
>>
>> pfam
>> ----
>>
>> gus> ga +run GUS::Common::Plugin::SubmitRow  
>> --attrlist=NAME,LOWERCASE_NAME
>> --valuelist="Pfam^^^pfam" --tablename=SRes::ExternalDatabase --commit
>>
>> SQL> select EXTERNAL_DATABASE_ID,NAME from sres.externaldatabase where
>> NAME='Pfam';
>> EXTERNAL_DATABASE_ID NAME
>>                    7     Pfam
>>
>> gus> ga +run GUS::Common::Plugin::SubmitRow
>> --attrlist=EXTERNAL_DATABASE_ID,VERSION,DOWNLOAD_URL
>> --valuelist="7^^^9.0^^^http://www.sanger.ac.uk/Software/Pfam/ 
>> ftp.shtml"
>> --tablename=SRes::ExternalDatabaseRelease --commit
>>
>> ga +run GUS::Common::Plugin::LoadPfam
>> --flat_file=/home/gus/pfam/Pfam-A.full --release=9.0
>>
>> Error --> needs an entry for the 'medline' database (not clear if  
>> data is
>> required for medline)
>>
>> This generic message comes up for each of the databases below:
>>    die "Unable to find most recent ExternalDatabaseRelease for
>> ExternalDatabase $name"
>>    if (not defined($relId));
>>
>>
>>
>> medline
>> -------
>>  ga +run GUS::Common::Plugin::SubmitRow --attrlist=NAME,LOWERCASE_NAME
>> --valuelist="MEDLINE^^^medline" --tablename=SRes::ExternalDatabase
>> --commit
>>
>>  ga +run GUS::Common::Plugin::SubmitRow
>> --attrlist=EXTERNAL_DATABASE_ID,VERSION --valuelist="8^^^unknown"
>> --tablename=SRes::ExternalDatabaseRelease --commit
>>
>>
>> prosite
>> -------
>>
>>  ga +run GUS::Common::Plugin::SubmitRow --attrlist=NAME,LOWERCASE_NAME
>> --valuelist="PROSITE^^^prosite" --tablename=SRes::ExternalDatabase
>> --commit
>>
>>  ga +run GUS::Common::Plugin::SubmitRow
>> --attrlist=EXTERNAL_DATABASE_ID,VERSION --valuelist="9^^^unknown"
>> --tablename=SRes::ExternalDatabaseRelease --commit
>>
>>
>> smart
>> -------
>>
>>  ga +run GUS::Common::Plugin::SubmitRow --attrlist=NAME,LOWERCASE_NAME
>> --valuelist="SMART^^^smart" --tablename=SRes::ExternalDatabase  
>> --commit
>>
>>  ga +run GUS::Common::Plugin::SubmitRow
>> --attrlist=EXTERNAL_DATABASE_ID,VERSION --valuelist="10^^^unknown"
>> --tablename=SRes::ExternalDatabaseRelease --commit
>>
>>
>> prints
>> ------
>>  ga +run GUS::Common::Plugin::SubmitRow --attrlist=NAME,LOWERCASE_NAME
>> --valuelist="PRINTS^^^prints" --tablename=SRes::ExternalDatabase  
>> --commit
>>
>>  ga +run GUS::Common::Plugin::SubmitRow
>> --attrlist=EXTERNAL_DATABASE_ID,VERSION --valuelist="11^^^unknown"
>> --tablename=SRes::ExternalDatabaseRelease --commit
>>
>> scops
>> -----
>>
>>  ga +run GUS::Common::Plugin::SubmitRow --attrlist=NAME,LOWERCASE_NAME
>> --valuelist="SCOP^^^scop" --tablename=SRes::ExternalDatabase --commit
>>
>>  ga +run GUS::Common::Plugin::SubmitRow
>> --attrlist=EXTERNAL_DATABASE_ID,VERSION --valuelist="12^^^unknown"
>> --tablename=SRes::ExternalDatabaseRelease --commit
>>
>> interpro
>> --------
>>
>>  ga +run GUS::Common::Plugin::SubmitRow --attrlist=NAME,LOWERCASE_NAME
>> --valuelist="INTERPRO^^^interpro" --tablename=SRes::ExternalDatabase
>> --commit
>>
>>  ga +run GUS::Common::Plugin::SubmitRow
>> --attrlist=EXTERNAL_DATABASE_ID,VERSION --valuelist="13^^^unknown"
>> --tablename=SRes::ExternalDatabaseRelease --commit
>>
>> pdb
>> ---
>>
>>  ga +run GUS::Common::Plugin::SubmitRow --attrlist=NAME,LOWERCASE_NAME
>> --valuelist="PDB^^^pdb" --tablename=SRes::ExternalDatabase --commit
>>
>>  ga +run GUS::Common::Plugin::SubmitRow
>> --attrlist=EXTERNAL_DATABASE_ID,VERSION --valuelist="14^^^unknown"
>> --tablename=SRes::ExternalDatabaseRelease --commit
>>
>>
>> homstrad
>> --------
>>  ga +run GUS::Common::Plugin::SubmitRow --attrlist=NAME,LOWERCASE_NAME
>> --valuelist="HOMSTRAD^^^homstrad" --tablename=SRes::ExternalDatabase
>> --commit
>>
>>  ga +run GUS::Common::Plugin::SubmitRow
>> --attrlist=EXTERNAL_DATABASE_ID,VERSION --valuelist="15^^^unknown"
>> --tablename=SRes::ExternalDatabaseRelease --commit
>>
>>
>> pfam-b
>> ------
>>  ga +run GUS::Common::Plugin::SubmitRow --attrlist=NAME,LOWERCASE_NAME
>> --valuelist="Pfam-B^^^pfam-b" --tablename=SRes::ExternalDatabase  
>> --commit
>>
>>  ga +run GUS::Common::Plugin::SubmitRow
>> --attrlist=EXTERNAL_DATABASE_ID,VERSION --valuelist="16^^^unknown"
>> --tablename=SRes::ExternalDatabaseRelease --commit
>>
>> mim
>> ___
>>  ga +run GUS::Common::Plugin::SubmitRow --attrlist=NAME,LOWERCASE_NAME
>> --valuelist="MIM^^^mim" --tablename=SRes::ExternalDatabase --commit
>>
>>  ga +run GUS::Common::Plugin::SubmitRow
>> --attrlist=EXTERNAL_DATABASE_ID,VERSION --valuelist="17^^^unknown"
>> --tablename=SRes::ExternalDatabaseRelease --commit
>>
>>
>> url
>> ---
>>  ga +run GUS::Common::Plugin::SubmitRow --attrlist=NAME,LOWERCASE_NAME
>> --valuelist="URL^^^url" --tablename=SRes::ExternalDatabase --commit
>>
>>  ga +run GUS::Common::Plugin::SubmitRow
>> --attrlist=EXTERNAL_DATABASE_ID,VERSION --valuelist="18^^^unknown"
>> --tablename=SRes::ExternalDatabaseRelease --commit
>>
>> merops
>> ------
>> ga +run GUS::Common::Plugin::SubmitRow --attrlist=NAME,LOWERCASE_NAME
>> --valuelist="MEROPS^^^merops" --tablename=SRes::ExternalDatabase  
>> --commit
>>
>>  ga +run GUS::Common::Plugin::SubmitRow
>> --attrlist=EXTERNAL_DATABASE_ID,VERSION --valuelist="19^^^unknown"
>> --tablename=SRes::ExternalDatabaseRelease --commit
>>
>> pfam expert
>> -----------
>> ga +run GUS::Common::Plugin::SubmitRow --attrlist=NAME,LOWERCASE_NAME
>> --valuelist="Pfam expert^^^pfam expert"  
>> --tablename=SRes::ExternalDatabase
>> --commit
>>
>>  ga +run GUS::Common::Plugin::SubmitRow
>> --attrlist=EXTERNAL_DATABASE_ID,VERSION --valuelist="20^^^unknown"
>> --tablename=SRes::ExternalDatabaseRelease --commit
>>
>>
>> cazy
>> ----
>> ga +run GUS::Common::Plugin::SubmitRow --attrlist=NAME,LOWERCASE_NAME
>> --valuelist="CAZy^^^cazy" --tablename=SRes::ExternalDatabase --commit
>>
>>  ga +run GUS::Common::Plugin::SubmitRow
>> --attrlist=EXTERNAL_DATABASE_ID,VERSION --valuelist="21^^^unknown"
>> --tablename=SRes::ExternalDatabaseRelease --commit
>>
>> load
>> ----
>> ga +run GUS::Common::Plugin::SubmitRow --attrlist=NAME,LOWERCASE_NAME
>> --valuelist="LOAD^^^load" --tablename=SRes::ExternalDatabase --commit
>>
>>  ga +run GUS::Common::Plugin::SubmitRow
>> --attrlist=EXTERNAL_DATABASE_ID,VERSION --valuelist="22^^^unknown"
>> --tablename=SRes::ExternalDatabaseRelease --commit
>>
>>
>> gus> ps -lfp 3601
>>   F S UID        PID  PPID  C PRI  NI ADDR    SZ WCHAN  STIME TTY
>> TIME CMD
>> 000 S gus       3601  2287  1  75       - 70391 schedu 13:10 pts/6
>> 00:04:46 /usr/bin/perl /home/gus/run/bin/ga +run
>> GUS::Common::Plugin::LoadPfam --flat_file=/home/gus/pfam/Pfam-A.full
>> --release=9.0
>>
>> gus> ga +run GUS::Common::Plugin::LoadPfam
>> --flat_file=/home/gus/pfam/Pfam-A.full --release=9.0
>> Loaded 5724 entries and 57986 database references from Pfam release  
>> 9.0.
>> Thu Jul 10 04:25:49 2003        RESULT  Loaded 5724 entries and 57986
>> database references from Pfam release 9.0.
>>
>> July 10, 2003
>>
>> NOTE: the above took about 14 hours to run without a commit.
>>
>> Here we go ...
>>
>>
>> gus> time ga +run GUS::Common::Plugin::LoadPfam
>> --flat_file=/home/gus/pfam/Pfam-A.full --release=9.0 --commit >&
>> loadpfam.out
>> 341.906u 28.548s 35:51.80 17.2% 0+0k 0+0io 1437pf+0w
>>
>>   ...
>> 5719: PF00100
>> 5720: PF05707
>> 5721: PF03367
>> 5722: PF00791
>> 5723: PF00569
>> Loaded 5724 entries and 55160 database references from Pfam release  
>> 9.0.
>> Thu Jul 10 11:58:20 2003 RESULT  Loaded 5724 entries and 55160  
>> database
>> references from Pfam release 9.0.
>>
>> LOADED OK. NOTE THA
>> T THERE WERE SOME DUPLICATE ENTRY MESSAGES.
>> NEED TO TRACK THESE DOWN -- see loadpfam.out  .
>>
>>
>>
>>
>>
>>
>
>
> -- 
> Sucheta Tripathy
> Virginia Bioinformatics Institute
> 1880 Pratt Drive,Bldg XV
> Virginia Tech.
> Blacksburg
> Virginia
> VA 24061
> phone-(540)231-8138
>
>
> -------------------------------------------------------
> This SF.net email is sponsored by: IBM Linux Tutorials.
> Become an expert in LINUX or just sharpen your skills.  Sign up for  
> IBM's
> Free Linux Tutorials.  Learn everything from the bash shell to sys  
> admin.
> Click now! http://ads.osdn.com/?ad_id=1278&alloc_id=3371&op=click
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>