[Gusdev-gusdev] Re: LoadPfam doubts

[Sucheta T. <su...@vb...>]

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
>> >> >>>
>> >> >
>> >> >
>> >> >
>> >> >
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>>
>> --
>> 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