Menu
▾
▴
gusdev-gusdev — Topics concerning GUS development
You can subscribe to this list here.
| 2002 |
Jan
|
Feb
|
Mar
|
Apr
|
May
|
Jun
(11) |
Jul
(34) |
Aug
(14) |
Sep
(10) |
Oct
(10) |
Nov
(11) |
Dec
(6) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 2003 |
Jan
(56) |
Feb
(76) |
Mar
(68) |
Apr
(11) |
May
(97) |
Jun
(16) |
Jul
(29) |
Aug
(35) |
Sep
(18) |
Oct
(32) |
Nov
(23) |
Dec
(77) |
| 2004 |
Jan
(52) |
Feb
(44) |
Mar
(55) |
Apr
(38) |
May
(106) |
Jun
(82) |
Jul
(76) |
Aug
(47) |
Sep
(36) |
Oct
(56) |
Nov
(46) |
Dec
(61) |
| 2005 |
Jan
(52) |
Feb
(118) |
Mar
(41) |
Apr
(40) |
May
(35) |
Jun
(99) |
Jul
(84) |
Aug
(104) |
Sep
(53) |
Oct
(107) |
Nov
(68) |
Dec
(30) |
| 2006 |
Jan
(19) |
Feb
(27) |
Mar
(24) |
Apr
(9) |
May
(22) |
Jun
(11) |
Jul
(34) |
Aug
(8) |
Sep
(15) |
Oct
(55) |
Nov
(16) |
Dec
(2) |
| 2007 |
Jan
(12) |
Feb
(4) |
Mar
(8) |
Apr
|
May
(19) |
Jun
(3) |
Jul
(1) |
Aug
(6) |
Sep
(12) |
Oct
(3) |
Nov
|
Dec
|
| 2008 |
Jan
(4) |
Feb
|
Mar
|
Apr
|
May
(1) |
Jun
(1) |
Jul
|
Aug
|
Sep
|
Oct
(1) |
Nov
|
Dec
(21) |
| 2009 |
Jan
|
Feb
(2) |
Mar
(1) |
Apr
|
May
(1) |
Jun
(8) |
Jul
|
Aug
|
Sep
|
Oct
|
Nov
|
Dec
|
| 2010 |
Jan
|
Feb
(1) |
Mar
(4) |
Apr
(3) |
May
|
Jun
|
Jul
|
Aug
|
Sep
|
Oct
|
Nov
|
Dec
|
| 2011 |
Jan
|
Feb
|
Mar
|
Apr
(4) |
May
(19) |
Jun
(14) |
Jul
(1) |
Aug
|
Sep
|
Oct
|
Nov
|
Dec
|
| 2012 |
Jan
|
Feb
|
Mar
(22) |
Apr
(12) |
May
|
Jun
|
Jul
|
Aug
|
Sep
|
Oct
|
Nov
|
Dec
|
| 2013 |
Jan
(2) |
Feb
|
Mar
|
Apr
|
May
|
Jun
|
Jul
|
Aug
|
Sep
|
Oct
(2) |
Nov
|
Dec
|
| 2015 |
Jan
|
Feb
|
Mar
|
Apr
|
May
(3) |
Jun
|
Jul
|
Aug
(2) |
Sep
|
Oct
|
Nov
|
Dec
(1) |
| 2016 |
Jan
(1) |
Feb
(1) |
Mar
|
Apr
(1) |
May
|
Jun
(2) |
Jul
(1) |
Aug
|
Sep
|
Oct
(1) |
Nov
(1) |
Dec
|
| 2017 |
Jan
|
Feb
|
Mar
|
Apr
|
May
(1) |
Jun
|
Jul
|
Aug
|
Sep
|
Oct
|
Nov
|
Dec
|
|
From: Sucheta T. <su...@vb...> - 2003-12-26 14:56:14
|
Hi Mathew,
I hope you received my earlier reply to the forum, but somehow it did not
appear in my mailbox, so I am resending.
------
From our experience with GUS installation, we had done build thrice(As can
be found in Terry Clark's documents).
Before building the first time you have to copy the original build.xml as
some other file(to be used later) and to the build.xml delete the 117-120
and 189-192(This number is actually 190-193 before deleting 117-120 lines)
lines.
The contents of these lines are:
<exec executable="generateGusObjects"
failonerror="true">
<arg value="--javaOrPerl=java"/>
</exec>
<exec executable="generateGusObjects"
failonerror="true">
<arg value="--javaOrPerl=perl"/>
</exec>
Then run build GUS install -append.
This will give you an error message saying
"Error in build.xml at 337 schema.prop file.
Then change the scema.prop file(from Terry Clark's documentation
appropriately) before building GUS for the second time.
Hope this helps.
Sucheta
--
Sucheta Tripathy
Virginia Bioinformatics Institute
1880 Pratt Drive,Bldg XV
Virginia Tech.
Blacksburg
Virginia
VA 24061
phone-(540)231-8138
|
|
From: Terry C. <tw...@cs...> - 2003-12-24 23:22:58
|
It looks like the alignment coordinates are
not stored by LoadPfam.pm. The coordinates
go to the bit bucket (I think)
360 # DR URL; http://www.gcrdb.uthscsa.edu/;
361 #
362 my $dbrefs = $entry->{'DR'};
363
364 foreach my $dbref (@$dbrefs) {
365 my($db, $id, $rest) = ($dbref =~ /^([^;]+);\s*([^;]+);(.*)$/);
366 die "Unable to parse $dbref" if (not defined($id));
by way of variable "$rest".
Terry
On 0, Sucheta Tripathy <su...@vb...> 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
|
|
From: Sucheta T. <su...@vb...> - 2003-12-24 20:38:22
|
Hi Matthew,
From our experience with GUS installation, we had done build thrice(As can
be found in Terry Clark's documents).
Before building the first time you have to copy the original build.xml as
some other file(to be used later) and to the build.xml delete the 117-120
and 189-192(This number is actually 190-193 before deleting 117-120 lines)
lines.
The contents of these lines are:
<exec executable="generateGusObjects"
failonerror="true">
<arg value="--javaOrPerl=java"/>
</exec>
<exec executable="generateGusObjects"
failonerror="true">
<arg value="--javaOrPerl=perl"/>
</exec>
Then run build GUS install -append.
This will give you an error message saying
"Error in build.xml at 337 schema.prop file.
Then change the scema.prop file(from Terry Clark's documentation
appropriately) before building GUS for the second time.
Hope this helps.
Sucheta
> Hi Matthew,
> I believe this is a know problem (you need to have a GUS instance to
> create a GUS instance) but there is a workaround. see section 2.4 of
> Terry Clark's installation
> guide.http://www.gusdb.org/documentation/installguide.html
> BTW, most of CBIL is on holiday until Jan 5 so you may not get much in
> the way of response from us until then.
> Cheers,
> Chris
>
>
> On Dec 23, 2003, at 8:50 PM, Matthew Hobbs wrote:
>
>> Hi,
>>
>> I am trying to set up a GUS based system. Having managed to set up an
>> Oracle
>> system suitable for prototyping I am now trying the GUS installation
>> but have
>> hit a snag when building 'install' and 'GUS' targets (see below).
>> The error
>> suggests that a table is not found but I thought this build was a
>> prerequistite for installing the GUS schema? i.e. I have made a GUS
>> database
>> but it hasn't got tables in it yet...
>>
>> Having spent so much effort with Oracle set up I'd really appreciate
>> any
>> advice on how to progess!
>>
>> Thanks very much,
>>
>>
>> Matthew
>>
>>
>> ant -f /home/matthew/GUS/projects/install/build.xml install -Dproj=GUS
>> -DtargetDir=/home/matthew/GUS/gushome -Dcomp=
>> -DprojectsDir=/home/matthew/
>> GUS/p
>> rojects -Dappend=true -logger org.apache.tools.ant.NoBannerLogger |
>> grep
>> ']'
>>
>> [echo] .
>> [echo] Installing CBIL/Bio
>> [echo] .
>> [echo] Installing CBIL/CSP
>> [echo] .
>> [echo] Installing CBIL/Util
>> [concat] Warning: Could not find any of the files specified in
>> concat task.
>> [echo] .
>> [echo] Installing GUS/Common
>> [echo] .
>> [echo] Installing GUS/DBAdmin
>> [echo] .
>> [echo] Installing GUS/GOPredict
>> [echo] .
>> [echo] Installing GUS/ObjRelP
>> [echo] generating Perl Objects
>> [exec] Reading properties from /home/matthew/.gus.properties
>> [exec] DBD::Oracle::db prepare failed: ORA-00942: table or view
>> does not
>> exist (DBD ERROR: OCIStmtExecute/Describe) [for Statement "select
>> d.name
>> ,t.name,t.is_view from Core.TableInfo t, Core.DatabaseInfo d where
>> d.database_id = t.database_id"] at
>> /home/matthew/GUS/gushome/lib/perl/GUS/
>> ObjRelP/D
>> biDbHandle.pm line 78.
>> [exec] Prepare FAILED: ORA-00942: table or view does not exist
>> (DBD
>> ERROR: OCIStmtExecute/Describe)
>> [exec] sql_cmd:
>> [exec] select d.name,t.name,t.is_view from Core.TableInfo t,
>> Core.DatabaseInfo d where d.database_id = t.database_id
>> [exec] Can't call method "execute" without a package or object
>> reference
>> at /home/matthew/GUS/gushome/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line
>> 79
>> .
>>
>> BUILD FAILED
>> file:/home/matthew/GUS/projects/GUS/build.xml:194: exec returned: 22
>>
>> Total time: 5 seconds
>>
>>
>>
>> --
>> Matthew Hobbs Research Fellow in Bioinformatics
>> Faculty of Veterinary Science
>> Building B19, University of Sydney, NSW 2006, Australia
>> Phone: +61 2 9351 3154 Fax: +61 2 93513957
>>
>>
>>
>> -------------------------------------------------------
>> 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
>>
>
>
>
> -------------------------------------------------------
> 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
|
|
From: Chris S. <sto...@pc...> - 2003-12-24 19:16:24
|
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 > |
|
From: Chris S. <sto...@pc...> - 2003-12-24 19:07:32
|
Hi Matthew, I believe this is a know problem (you need to have a GUS instance to create a GUS instance) but there is a workaround. see section 2.4 of Terry Clark's installation guide.http://www.gusdb.org/documentation/installguide.html BTW, most of CBIL is on holiday until Jan 5 so you may not get much in the way of response from us until then. Cheers, Chris On Dec 23, 2003, at 8:50 PM, Matthew Hobbs wrote: > Hi, > > I am trying to set up a GUS based system. Having managed to set up an > Oracle > system suitable for prototyping I am now trying the GUS installation > but have > hit a snag when building 'install' and 'GUS' targets (see below). > The error > suggests that a table is not found but I thought this build was a > prerequistite for installing the GUS schema? i.e. I have made a GUS > database > but it hasn't got tables in it yet... > > Having spent so much effort with Oracle set up I'd really appreciate > any > advice on how to progess! > > Thanks very much, > > > Matthew > > > ant -f /home/matthew/GUS/projects/install/build.xml install -Dproj=GUS > -DtargetDir=/home/matthew/GUS/gushome -Dcomp= > -DprojectsDir=/home/matthew/ > GUS/p > rojects -Dappend=true -logger org.apache.tools.ant.NoBannerLogger | > grep > ']' > > [echo] . > [echo] Installing CBIL/Bio > [echo] . > [echo] Installing CBIL/CSP > [echo] . > [echo] Installing CBIL/Util > [concat] Warning: Could not find any of the files specified in > concat task. > [echo] . > [echo] Installing GUS/Common > [echo] . > [echo] Installing GUS/DBAdmin > [echo] . > [echo] Installing GUS/GOPredict > [echo] . > [echo] Installing GUS/ObjRelP > [echo] generating Perl Objects > [exec] Reading properties from /home/matthew/.gus.properties > [exec] DBD::Oracle::db prepare failed: ORA-00942: table or view > does not > exist (DBD ERROR: OCIStmtExecute/Describe) [for Statement "select > d.name > ,t.name,t.is_view from Core.TableInfo t, Core.DatabaseInfo d where > d.database_id = t.database_id"] at > /home/matthew/GUS/gushome/lib/perl/GUS/ > ObjRelP/D > biDbHandle.pm line 78. > [exec] Prepare FAILED: ORA-00942: table or view does not exist > (DBD > ERROR: OCIStmtExecute/Describe) > [exec] sql_cmd: > [exec] select d.name,t.name,t.is_view from Core.TableInfo t, > Core.DatabaseInfo d where d.database_id = t.database_id > [exec] Can't call method "execute" without a package or object > reference > at /home/matthew/GUS/gushome/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line > 79 > . > > BUILD FAILED > file:/home/matthew/GUS/projects/GUS/build.xml:194: exec returned: 22 > > Total time: 5 seconds > > > > -- > Matthew Hobbs Research Fellow in Bioinformatics > Faculty of Veterinary Science > Building B19, University of Sydney, NSW 2006, Australia > Phone: +61 2 9351 3154 Fax: +61 2 93513957 > > > > ------------------------------------------------------- > 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 > |
|
From: Sucheta T. <su...@vb...> - 2003-12-24 13:23:41
|
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 |
|
From: Terry C. <tw...@cs...> - 2003-12-24 06:35:03
|
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 0 - 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 THAT THERE WERE SOME DUPLICATE ENTRY MESSAGES. NEED TO TRACK THESE DOWN -- see loadpfam.out . |
|
From: Matthew H. <mat...@ve...> - 2003-12-24 01:50:13
|
Hi,
I am trying to set up a GUS based system. Having managed to set up an Oracle
system suitable for prototyping I am now trying the GUS installation but have
hit a snag when building 'install' and 'GUS' targets (see below). The error
suggests that a table is not found but I thought this build was a
prerequistite for installing the GUS schema? i.e. I have made a GUS database
but it hasn't got tables in it yet...
Having spent so much effort with Oracle set up I'd really appreciate any
advice on how to progess!
Thanks very much,
Matthew
ant -f /home/matthew/GUS/projects/install/build.xml install -Dproj=GUS
-DtargetDir=/home/matthew/GUS/gushome -Dcomp= -DprojectsDir=/home/matthew/
GUS/p
rojects -Dappend=true -logger org.apache.tools.ant.NoBannerLogger | grep
']'
[echo] .
[echo] Installing CBIL/Bio
[echo] .
[echo] Installing CBIL/CSP
[echo] .
[echo] Installing CBIL/Util
[concat] Warning: Could not find any of the files specified in concat task.
[echo] .
[echo] Installing GUS/Common
[echo] .
[echo] Installing GUS/DBAdmin
[echo] .
[echo] Installing GUS/GOPredict
[echo] .
[echo] Installing GUS/ObjRelP
[echo] generating Perl Objects
[exec] Reading properties from /home/matthew/.gus.properties
[exec] DBD::Oracle::db prepare failed: ORA-00942: table or view does not
exist (DBD ERROR: OCIStmtExecute/Describe) [for Statement "select d.name
,t.name,t.is_view from Core.TableInfo t, Core.DatabaseInfo d where
d.database_id = t.database_id"] at /home/matthew/GUS/gushome/lib/perl/GUS/
ObjRelP/D
biDbHandle.pm line 78.
[exec] Prepare FAILED: ORA-00942: table or view does not exist (DBD
ERROR: OCIStmtExecute/Describe)
[exec] sql_cmd:
[exec] select d.name,t.name,t.is_view from Core.TableInfo t,
Core.DatabaseInfo d where d.database_id = t.database_id
[exec] Can't call method "execute" without a package or object reference
at /home/matthew/GUS/gushome/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 79
.
BUILD FAILED
file:/home/matthew/GUS/projects/GUS/build.xml:194: exec returned: 22
Total time: 5 seconds
--
Matthew Hobbs Research Fellow in Bioinformatics
Faculty of Veterinary Science
Building B19, University of Sydney, NSW 2006, Australia
Phone: +61 2 9351 3154 Fax: +61 2 93513957
|
|
From: sucheta T. <su...@vb...> - 2003-12-23 15:34:28
|
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 |
|
From: Terry C. <tw...@cs...> - 2003-12-23 04:44:31
|
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 |
|
From: Steve F. <sfi...@pc...> - 2003-12-19 21:57:25
|
I think the best way to answer this would by phone. however, i am leaving for vacation in an hour, so it would be best to wait till after the holiday. i am attaching our pipeline to build the DoTS dataset used by the allgenes site. you may be able to understand what we have done by looking carefully at it. steve sucheta Tripathy wrote: >Hi Steve, > >I have several questions regarding the pipeline programs that can be run >in GUS. > >We have sequences that are not annotated (both genomic and EST sequences). >We want them to be run through cleaning, assembly protocols followed by >several other programs for annotation. > >Apart from that for the genome sequences we have extra requirements like >storing the data from each prediction program, having EST-genome mapped >data, intron, exon data and so on... > >Is it possible to run all these programs through the pipeline, or there is >a list of programs that can only be passed through the pipeline(If so, >where can I look for them). > >In order to put the annotated data into database, do I have to use other >plugins or the pipeline looks after them. > >Thanks > >Sucheta > > > > > |
|
From: sucheta T. <su...@vb...> - 2003-12-19 21:42:05
|
Hi Steve, I have several questions regarding the pipeline programs that can be run in GUS. We have sequences that are not annotated (both genomic and EST sequences). We want them to be run through cleaning, assembly protocols followed by several other programs for annotation. Apart from that for the genome sequences we have extra requirements like storing the data from each prediction program, having EST-genome mapped data, intron, exon data and so on... Is it possible to run all these programs through the pipeline, or there is a list of programs that can only be passed through the pipeline(If so, where can I look for them). In order to put the annotated data into database, do I have to use other plugins or the pipeline looks after them. Thanks Sucheta -- Sucheta Tripathy Virginia Bioinformatics Institute 1880 pratt drive,Bldg XV Virginia tech. Blacksburg Virginia VA 24061 phone-(540)231-8138 |
|
From: Terry C. <tw...@cs...> - 2003-12-19 00:22:21
|
You're right, Keith. I just checked with an Oracle field rep: the 9i license you cited appears to be the least restrictive for no-$$ license options that are available. Although I find the level of restriction annoying (the UChicago sitewide Oracle arrangement aside), the free-use terms of the freely available Oracle distribution can go a long way in setting up and prototyping a GUS based system. I might add, Oracle had/has a research incentive program for reducing some initial licensing costs. When I used this program a few years ago, it involved submitting a proposal to Oracle. Terry On 0, Keith James <kd...@sa...> wrote: > >>>>> "Terry" == Terry Clark <tw...@cs...> writes: > > Terry> Matthew, there is a free Oracle release for Linux. GUS > Terry> works fine with this. > > I think that you will be limited as to what you can do with this. The > licenses I have seen specifically prohibit use of the free versions > for internal data processing (or anything but the development of a > single non-production prototype). > > Not being 100% sure about the licensing status (especially for > personal editions) I've been searching the Oracle site. All the > downloads I found involved agreement to their developer license which > includes this statement: > > "We grant you a nonexclusive, nontransferable limited license to use > the programs only for the purpose of developing a single prototype of > your application, and not for any other purpose. If you use the > application you develop under this license for any internal data > processing or for any commercial or production purposes, or you want > to use the programs for any purpose other than as permitted under this > agreement, you must contact us, or an Oracle reseller, to obtain the > appropriate license. We may audit your use of the programs." > > If anyone knows of a less restrictive Oracle release I would be happy > to hear about it. > > Keith > > -- > > - Keith James <kd...@sa...> Microarray Facility, Team 65 - > - The Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK - > > > ------------------------------------------------------- > 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 |
|
From: Steve F. <sfi...@pc...> - 2003-12-18 14:51:15
|
one more thing to mention on this thread. while i don't know much about the free version, when we last checked there were reasonably affordable oracle licenses available. steve Keith James wrote: >>>>>>"Terry" == Terry Clark <tw...@cs...> writes: >>>>>> >>>>>> > > Terry> Matthew, there is a free Oracle release for Linux. GUS > Terry> works fine with this. > >I think that you will be limited as to what you can do with this. The >licenses I have seen specifically prohibit use of the free versions >for internal data processing (or anything but the development of a >single non-production prototype). > >Not being 100% sure about the licensing status (especially for >personal editions) I've been searching the Oracle site. All the >downloads I found involved agreement to their developer license which >includes this statement: > >"We grant you a nonexclusive, nontransferable limited license to use >the programs only for the purpose of developing a single prototype of >your application, and not for any other purpose. If you use the >application you develop under this license for any internal data >processing or for any commercial or production purposes, or you want >to use the programs for any purpose other than as permitted under this >agreement, you must contact us, or an Oracle reseller, to obtain the >appropriate license. We may audit your use of the programs." > >If anyone knows of a less restrictive Oracle release I would be happy >to hear about it. > >Keith > > > |
|
From: Elisabetta M. <man...@pc...> - 2003-12-18 14:33:29
|
I think it's best that you use UpdateGusFromXML. If I recall correctly the UpdateGusFromCla was only implementing part of the functionality of UpdateGusFromXML. I think UPdateGusFromCla can be considered deprecated. Elisabetta On Thu, 18 Dec 2003, sucheta Tripathy wrote: > Hi Steve, > > Thanks for the suggestion. I also tried UpdateGusFromCla plugin. But not > sure if I should use it. It looks like the program ends successfully, but > does not update any value. > > Here is the snapshot: > ===================== > > >>ga GUS::Common::Plugin::UpdateGusFromCla --tablename > >>SRes::ExternalDatabase --at > >>trlist external_database_id,name,lowercase_name --valuelist > >>"16^^^PfamA^^^pfama" > >> --refresh --verbose --commit > >> > >>It looks like the program ends normally, but the database does not get > >>updated. > >> > >>Following is the output: > >>======================== > >>Reading properties from > >> /home/apps/GUS/dev/gushome/config/GUS-PluginMgr.prop > >>Reading properties from /home/apps/GUS/dev/.gus.properties > >>Wed Dec 17 14:58:55 2003 ALGINVID 102 > >>Wed Dec 17 14:58:55 2003 ARGS algoinvo 1 > >>Wed Dec 17 14:58:55 2003 ARGS attrlist > >>external_database_id,nam > >>e,lowercase_name > >>Wed Dec 17 14:58:55 2003 ARGS comment > >>Wed Dec 17 14:58:55 2003 ARGS commit 1 > >>Wed Dec 17 14:58:55 2003 ARGS debug > >>Wed Dec 17 14:58:55 2003 ARGS group > >>Wed Dec 17 14:58:55 2003 ARGS gusconfigfile > >>/home/apps/GUS/dev/.gus. > >>properties > >>Wed Dec 17 14:58:55 2003 ARGS project > >>Wed Dec 17 14:58:55 2003 ARGS refresh 1 > >>Wed Dec 17 14:58:55 2003 ARGS sqlVerbose > >>Wed Dec 17 14:58:55 2003 ARGS tablename > >>SRes::ExternalDatabase > >>Wed Dec 17 14:58:55 2003 ARGS usage > >>Wed Dec 17 14:58:55 2003 ARGS user > >>Wed Dec 17 14:58:55 2003 ARGS valuelist > >> 16^^^PfamA^^^pfama > >>Wed Dec 17 14:58:55 2003 ARGS verbose 1 > >>Wed Dec 17 14:58:55 2003 ARGS veryVerbose > >>Wed Dec 17 14:58:55 2003 COMMIT commit on > >>Wed Dec 17 14:58:55 2003 Result primary key is found in database, > >>doing > >>update > >>name Pfa > > > Any comments. > > Sucheta > > Sucheta- > > > > it does look like there is a flaw in SubmitRow (I wrote it!) which > > doesn't properly handle inserting. > > > > As a workaround, try UdateGusFromXML > > > > To see what the xml should look like, use printXML to print out an > > existing row from that table > > > > steve > > > > sucheta Tripathy wrote: > > > >>Hi, > >> > >>We have been trying to update some data into GUS using the SubmitRow > >> plugin. > >>Apparently from the first description line it appears the --refresh > >> option > >>updates the data, so we used the following option: > >> > >>ga GUS::Common::Plugin::SubmitRow --tablename SRes::ExternalDatabase > >>--attrlist > >> external_database_id,name,lowercase_name --valuelist > >> "16^^^PfamA^^^pfama" > >>--ref > >>resh --verbose --commit > >> > >>Instead of executing the sql statement as update it says: insert > >> into..... > >> > >>It gives the following error: > >>============================= > >> > >>Wed Dec 17 14:31:26 2003 ALGINVID 98 > >>Wed Dec 17 14:31:26 2003 COMMIT commit on > >>DBD::Oracle::st execute failed: ORA-00001: unique constraint > >>(SRES.PK_EXTERNALDA > >>TABASE) violated (DBD ERROR: OCIStmtExecute) [for Statement " > >> INSERT INTO SRes.ExternalDatabase ( other_read, group_write, > >>group_read, lo > >>wercase_name, name, user_read, row_user_id, external_database_id, > >>modification_d > >>ate, other_write, row_project_id, row_alg_invocation_id, row_group_id, > >>user_writ > >>e ) > >> VALUES ( ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? ) " with > >>ParamVal > >>ues: :p5='PfamA', :p6='1', :p3='1', :p12='1', :p7='1', :p1='1', :p8='16', > >>:p4='p > >>fama', :p10='1', :p9='0', :p13='1', :p11='98', :p2='1'] at > >>/home/apps/GUS/dev/gu > >>shome/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 145. > >>========================================================================== > >> > >>SO I tried another plugin UpdateGusFromCla > >>using the following option: > >> > >>ga GUS::Common::Plugin::UpdateGusFromCla --tablename > >>SRes::ExternalDatabase --at > >>trlist external_database_id,name,lowercase_name --valuelist > >>"16^^^PfamA^^^pfama" > >> --refresh --verbose --commit > >> > >>It looks like the program ends normally, but the database does not get > >>updated. > >> > >>Following is the output: > >>======================== > >>Reading properties from > >> /home/apps/GUS/dev/gushome/config/GUS-PluginMgr.prop > >>Reading properties from /home/apps/GUS/dev/.gus.properties > >>Wed Dec 17 14:58:55 2003 ALGINVID 102 > >>Wed Dec 17 14:58:55 2003 ARGS algoinvo 1 > >>Wed Dec 17 14:58:55 2003 ARGS attrlist > >>external_database_id,nam > >>e,lowercase_name > >>Wed Dec 17 14:58:55 2003 ARGS comment > >>Wed Dec 17 14:58:55 2003 ARGS commit 1 > >>Wed Dec 17 14:58:55 2003 ARGS debug > >>Wed Dec 17 14:58:55 2003 ARGS group > >>Wed Dec 17 14:58:55 2003 ARGS gusconfigfile > >>/home/apps/GUS/dev/.gus. > >>properties > >>Wed Dec 17 14:58:55 2003 ARGS project > >>Wed Dec 17 14:58:55 2003 ARGS refresh 1 > >>Wed Dec 17 14:58:55 2003 ARGS sqlVerbose > >>Wed Dec 17 14:58:55 2003 ARGS tablename > >>SRes::ExternalDatabase > >>Wed Dec 17 14:58:55 2003 ARGS usage > >>Wed Dec 17 14:58:55 2003 ARGS user > >>Wed Dec 17 14:58:55 2003 ARGS valuelist > >> 16^^^PfamA^^^pfama > >>Wed Dec 17 14:58:55 2003 ARGS verbose 1 > >>Wed Dec 17 14:58:55 2003 ARGS veryVerbose > >>Wed Dec 17 14:58:55 2003 COMMIT commit on > >>Wed Dec 17 14:58:55 2003 Result primary key is found in database, > >>doing > >>update > >>name PfamA > >>lowercase_name pfama > >>Wed Dec 17 14:58:55 2003 RESULT > >> > >>So, Now I am in doubt whether I am using the correct plugin(s). > >>Are there any plugins which does the database update job?Do I need to do > >>it at the SQL commandline. > >> > >>Thanks > >> > >>Sucheta > >> > >> > > > > > -- Elisabetta Manduchi Computational Biology and Informatics Laboratory Center for Bioinformatics University of Pennsylvania 1428 Blockley Hall 423 Guardian Drive Philadelphia, PA 19104-6021 phone: 215-573-4408 fax: 215 573-3111 email: man...@pc... web: http://www.cbil.upenn.edu/~manduchi --- |
|
From: sucheta T. <su...@vb...> - 2003-12-18 14:27:20
|
Hi Steve, Thanks for the suggestion. I also tried UpdateGusFromCla plugin. But not sure if I should use it. It looks like the program ends successfully, but does not update any value. Here is the snapshot: ===================== >>ga GUS::Common::Plugin::UpdateGusFromCla --tablename >>SRes::ExternalDatabase --at >>trlist external_database_id,name,lowercase_name --valuelist >>"16^^^PfamA^^^pfama" >> --refresh --verbose --commit >> >>It looks like the program ends normally, but the database does not get >>updated. >> >>Following is the output: >>======================== >>Reading properties from >> /home/apps/GUS/dev/gushome/config/GUS-PluginMgr.prop >>Reading properties from /home/apps/GUS/dev/.gus.properties >>Wed Dec 17 14:58:55 2003 ALGINVID 102 >>Wed Dec 17 14:58:55 2003 ARGS algoinvo 1 >>Wed Dec 17 14:58:55 2003 ARGS attrlist >>external_database_id,nam >>e,lowercase_name >>Wed Dec 17 14:58:55 2003 ARGS comment >>Wed Dec 17 14:58:55 2003 ARGS commit 1 >>Wed Dec 17 14:58:55 2003 ARGS debug >>Wed Dec 17 14:58:55 2003 ARGS group >>Wed Dec 17 14:58:55 2003 ARGS gusconfigfile >>/home/apps/GUS/dev/.gus. >>properties >>Wed Dec 17 14:58:55 2003 ARGS project >>Wed Dec 17 14:58:55 2003 ARGS refresh 1 >>Wed Dec 17 14:58:55 2003 ARGS sqlVerbose >>Wed Dec 17 14:58:55 2003 ARGS tablename >>SRes::ExternalDatabase >>Wed Dec 17 14:58:55 2003 ARGS usage >>Wed Dec 17 14:58:55 2003 ARGS user >>Wed Dec 17 14:58:55 2003 ARGS valuelist >> 16^^^PfamA^^^pfama >>Wed Dec 17 14:58:55 2003 ARGS verbose 1 >>Wed Dec 17 14:58:55 2003 ARGS veryVerbose >>Wed Dec 17 14:58:55 2003 COMMIT commit on >>Wed Dec 17 14:58:55 2003 Result primary key is found in database, >>doing >>update >>name Pfa Any comments. Sucheta > Sucheta- > > it does look like there is a flaw in SubmitRow (I wrote it!) which > doesn't properly handle inserting. > > As a workaround, try UdateGusFromXML > > To see what the xml should look like, use printXML to print out an > existing row from that table > > steve > > sucheta Tripathy wrote: > >>Hi, >> >>We have been trying to update some data into GUS using the SubmitRow >> plugin. >>Apparently from the first description line it appears the --refresh >> option >>updates the data, so we used the following option: >> >>ga GUS::Common::Plugin::SubmitRow --tablename SRes::ExternalDatabase >>--attrlist >> external_database_id,name,lowercase_name --valuelist >> "16^^^PfamA^^^pfama" >>--ref >>resh --verbose --commit >> >>Instead of executing the sql statement as update it says: insert >> into..... >> >>It gives the following error: >>============================= >> >>Wed Dec 17 14:31:26 2003 ALGINVID 98 >>Wed Dec 17 14:31:26 2003 COMMIT commit on >>DBD::Oracle::st execute failed: ORA-00001: unique constraint >>(SRES.PK_EXTERNALDA >>TABASE) violated (DBD ERROR: OCIStmtExecute) [for Statement " >> INSERT INTO SRes.ExternalDatabase ( other_read, group_write, >>group_read, lo >>wercase_name, name, user_read, row_user_id, external_database_id, >>modification_d >>ate, other_write, row_project_id, row_alg_invocation_id, row_group_id, >>user_writ >>e ) >> VALUES ( ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? ) " with >>ParamVal >>ues: :p5='PfamA', :p6='1', :p3='1', :p12='1', :p7='1', :p1='1', :p8='16', >>:p4='p >>fama', :p10='1', :p9='0', :p13='1', :p11='98', :p2='1'] at >>/home/apps/GUS/dev/gu >>shome/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 145. >>========================================================================== >> >>SO I tried another plugin UpdateGusFromCla >>using the following option: >> >>ga GUS::Common::Plugin::UpdateGusFromCla --tablename >>SRes::ExternalDatabase --at >>trlist external_database_id,name,lowercase_name --valuelist >>"16^^^PfamA^^^pfama" >> --refresh --verbose --commit >> >>It looks like the program ends normally, but the database does not get >>updated. >> >>Following is the output: >>======================== >>Reading properties from >> /home/apps/GUS/dev/gushome/config/GUS-PluginMgr.prop >>Reading properties from /home/apps/GUS/dev/.gus.properties >>Wed Dec 17 14:58:55 2003 ALGINVID 102 >>Wed Dec 17 14:58:55 2003 ARGS algoinvo 1 >>Wed Dec 17 14:58:55 2003 ARGS attrlist >>external_database_id,nam >>e,lowercase_name >>Wed Dec 17 14:58:55 2003 ARGS comment >>Wed Dec 17 14:58:55 2003 ARGS commit 1 >>Wed Dec 17 14:58:55 2003 ARGS debug >>Wed Dec 17 14:58:55 2003 ARGS group >>Wed Dec 17 14:58:55 2003 ARGS gusconfigfile >>/home/apps/GUS/dev/.gus. >>properties >>Wed Dec 17 14:58:55 2003 ARGS project >>Wed Dec 17 14:58:55 2003 ARGS refresh 1 >>Wed Dec 17 14:58:55 2003 ARGS sqlVerbose >>Wed Dec 17 14:58:55 2003 ARGS tablename >>SRes::ExternalDatabase >>Wed Dec 17 14:58:55 2003 ARGS usage >>Wed Dec 17 14:58:55 2003 ARGS user >>Wed Dec 17 14:58:55 2003 ARGS valuelist >> 16^^^PfamA^^^pfama >>Wed Dec 17 14:58:55 2003 ARGS verbose 1 >>Wed Dec 17 14:58:55 2003 ARGS veryVerbose >>Wed Dec 17 14:58:55 2003 COMMIT commit on >>Wed Dec 17 14:58:55 2003 Result primary key is found in database, >>doing >>update >>name PfamA >>lowercase_name pfama >>Wed Dec 17 14:58:55 2003 RESULT >> >>So, Now I am in doubt whether I am using the correct plugin(s). >>Are there any plugins which does the database update job?Do I need to do >>it at the SQL commandline. >> >>Thanks >> >>Sucheta >> >> > -- Sucheta Tripathy Virginia Bioinformatics Institute 1880 pratt drive,Bldg XV Virginia tech. Blacksburg Virginia VA 24061 phone-(540)231-8138 |
|
From: Keith J. <kd...@sa...> - 2003-12-18 12:57:11
|
>>>>> "Terry" == Terry Clark <tw...@cs...> writes:
Terry> Matthew, there is a free Oracle release for Linux. GUS
Terry> works fine with this.
I think that you will be limited as to what you can do with this. The
licenses I have seen specifically prohibit use of the free versions
for internal data processing (or anything but the development of a
single non-production prototype).
Not being 100% sure about the licensing status (especially for
personal editions) I've been searching the Oracle site. All the
downloads I found involved agreement to their developer license which
includes this statement:
"We grant you a nonexclusive, nontransferable limited license to use
the programs only for the purpose of developing a single prototype of
your application, and not for any other purpose. If you use the
application you develop under this license for any internal data
processing or for any commercial or production purposes, or you want
to use the programs for any purpose other than as permitted under this
agreement, you must contact us, or an Oracle reseller, to obtain the
appropriate license. We may audit your use of the programs."
If anyone knows of a less restrictive Oracle release I would be happy
to hear about it.
Keith
--
- Keith James <kd...@sa...> Microarray Facility, Team 65 -
- The Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK -
|
|
From: Elisabetta M. <man...@pc...> - 2003-12-18 02:06:11
|
Matthew, there is a group I know of that is working on porting GUS to PostgreSQL. They started on this project fairly recently, I'm not sure about the timeframe. Elisabetta On Thu, 18 Dec 2003, Matthew Hobbs wrote: > Hi, > > I am very interested in GUS but am currently unable to use it as I don't have > Oracle available to me. I have read in this list that it is proposed to > develop versions of GUS that might work with MySQL or Postgresql and was just > wondering if anyone can give me please an indication of a timeframe in which > this might happen? > > Thanks very much, > > Matthew > -- Elisabetta Manduchi Computational Biology and Informatics Laboratory Center for Bioinformatics University of Pennsylvania 1428 Blockley Hall 423 Guardian Drive Philadelphia, PA 19104-6021 phone: 215-573-4408 fax: 215 573-3111 email: man...@pc... web: http://www.cbil.upenn.edu/~manduchi --- |
|
From: Terry C. <tw...@cs...> - 2003-12-18 00:23:44
|
Matthew, there is a free Oracle release for Linux. GUS works fine with this. Terry On 0, Matthew Hobbs <mat...@ve...> wrote: > Hi, > > I am very interested in GUS but am currently unable to use it as I don't have > Oracle available to me. I have read in this list that it is proposed to > develop versions of GUS that might work with MySQL or Postgresql and was just > wondering if anyone can give me please an indication of a timeframe in which > this might happen? > > Thanks very much, > > Matthew > -- > Matthew Hobbs Research Fellow in Bioinformatics > Faculty of Veterinary Science > Building B19, University of Sydney, NSW 2006, Australia > Phone: +61 2 9351 3154 Fax: +61 2 93513957 > > > > ------------------------------------------------------- > 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 |
|
From: Matthew H. <mat...@ve...> - 2003-12-17 23:37:34
|
Hi, I am very interested in GUS but am currently unable to use it as I don't have Oracle available to me. I have read in this list that it is proposed to develop versions of GUS that might work with MySQL or Postgresql and was just wondering if anyone can give me please an indication of a timeframe in which this might happen? Thanks very much, Matthew -- Matthew Hobbs Research Fellow in Bioinformatics Faculty of Veterinary Science Building B19, University of Sydney, NSW 2006, Australia Phone: +61 2 9351 3154 Fax: +61 2 93513957 |
|
From: Steve F. <sfi...@pc...> - 2003-12-17 21:30:07
|
Sucheta- it does look like there is a flaw in SubmitRow (I wrote it!) which doesn't properly handle inserting. As a workaround, try UdateGusFromXML To see what the xml should look like, use printXML to print out an existing row from that table steve sucheta Tripathy wrote: >Hi, > >We have been trying to update some data into GUS using the SubmitRow plugin. >Apparently from the first description line it appears the --refresh option >updates the data, so we used the following option: > >ga GUS::Common::Plugin::SubmitRow --tablename SRes::ExternalDatabase >--attrlist > external_database_id,name,lowercase_name --valuelist "16^^^PfamA^^^pfama" >--ref >resh --verbose --commit > >Instead of executing the sql statement as update it says: insert into..... > >It gives the following error: >============================= > >Wed Dec 17 14:31:26 2003 ALGINVID 98 >Wed Dec 17 14:31:26 2003 COMMIT commit on >DBD::Oracle::st execute failed: ORA-00001: unique constraint >(SRES.PK_EXTERNALDA >TABASE) violated (DBD ERROR: OCIStmtExecute) [for Statement " > INSERT INTO SRes.ExternalDatabase ( other_read, group_write, >group_read, lo >wercase_name, name, user_read, row_user_id, external_database_id, >modification_d >ate, other_write, row_project_id, row_alg_invocation_id, row_group_id, >user_writ >e ) > VALUES ( ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? ) " with >ParamVal >ues: :p5='PfamA', :p6='1', :p3='1', :p12='1', :p7='1', :p1='1', :p8='16', >:p4='p >fama', :p10='1', :p9='0', :p13='1', :p11='98', :p2='1'] at >/home/apps/GUS/dev/gu >shome/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 145. >========================================================================== > >SO I tried another plugin UpdateGusFromCla >using the following option: > >ga GUS::Common::Plugin::UpdateGusFromCla --tablename >SRes::ExternalDatabase --at >trlist external_database_id,name,lowercase_name --valuelist >"16^^^PfamA^^^pfama" > --refresh --verbose --commit > >It looks like the program ends normally, but the database does not get >updated. > >Following is the output: >======================== >Reading properties from /home/apps/GUS/dev/gushome/config/GUS-PluginMgr.prop >Reading properties from /home/apps/GUS/dev/.gus.properties >Wed Dec 17 14:58:55 2003 ALGINVID 102 >Wed Dec 17 14:58:55 2003 ARGS algoinvo 1 >Wed Dec 17 14:58:55 2003 ARGS attrlist >external_database_id,nam >e,lowercase_name >Wed Dec 17 14:58:55 2003 ARGS comment >Wed Dec 17 14:58:55 2003 ARGS commit 1 >Wed Dec 17 14:58:55 2003 ARGS debug >Wed Dec 17 14:58:55 2003 ARGS group >Wed Dec 17 14:58:55 2003 ARGS gusconfigfile >/home/apps/GUS/dev/.gus. >properties >Wed Dec 17 14:58:55 2003 ARGS project >Wed Dec 17 14:58:55 2003 ARGS refresh 1 >Wed Dec 17 14:58:55 2003 ARGS sqlVerbose >Wed Dec 17 14:58:55 2003 ARGS tablename >SRes::ExternalDatabase >Wed Dec 17 14:58:55 2003 ARGS usage >Wed Dec 17 14:58:55 2003 ARGS user >Wed Dec 17 14:58:55 2003 ARGS valuelist 16^^^PfamA^^^pfama >Wed Dec 17 14:58:55 2003 ARGS verbose 1 >Wed Dec 17 14:58:55 2003 ARGS veryVerbose >Wed Dec 17 14:58:55 2003 COMMIT commit on >Wed Dec 17 14:58:55 2003 Result primary key is found in database, >doing >update >name PfamA >lowercase_name pfama >Wed Dec 17 14:58:55 2003 RESULT > >So, Now I am in doubt whether I am using the correct plugin(s). >Are there any plugins which does the database update job?Do I need to do >it at the SQL commandline. > >Thanks > >Sucheta > > |
|
From: sucheta T. <su...@vb...> - 2003-12-17 20:59:03
|
Hi,
We have been trying to update some data into GUS using the SubmitRow plugin.
Apparently from the first description line it appears the --refresh option
updates the data, so we used the following option:
ga GUS::Common::Plugin::SubmitRow --tablename SRes::ExternalDatabase
--attrlist
external_database_id,name,lowercase_name --valuelist "16^^^PfamA^^^pfama"
--ref
resh --verbose --commit
Instead of executing the sql statement as update it says: insert into.....
It gives the following error:
=============================
Wed Dec 17 14:31:26 2003 ALGINVID 98
Wed Dec 17 14:31:26 2003 COMMIT commit on
DBD::Oracle::st execute failed: ORA-00001: unique constraint
(SRES.PK_EXTERNALDA
TABASE) violated (DBD ERROR: OCIStmtExecute) [for Statement "
INSERT INTO SRes.ExternalDatabase ( other_read, group_write,
group_read, lo
wercase_name, name, user_read, row_user_id, external_database_id,
modification_d
ate, other_write, row_project_id, row_alg_invocation_id, row_group_id,
user_writ
e )
VALUES ( ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? ) " with
ParamVal
ues: :p5='PfamA', :p6='1', :p3='1', :p12='1', :p7='1', :p1='1', :p8='16',
:p4='p
fama', :p10='1', :p9='0', :p13='1', :p11='98', :p2='1'] at
/home/apps/GUS/dev/gu
shome/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 145.
==========================================================================
SO I tried another plugin UpdateGusFromCla
using the following option:
ga GUS::Common::Plugin::UpdateGusFromCla --tablename
SRes::ExternalDatabase --at
trlist external_database_id,name,lowercase_name --valuelist
"16^^^PfamA^^^pfama"
--refresh --verbose --commit
It looks like the program ends normally, but the database does not get
updated.
Following is the output:
========================
Reading properties from /home/apps/GUS/dev/gushome/config/GUS-PluginMgr.prop
Reading properties from /home/apps/GUS/dev/.gus.properties
Wed Dec 17 14:58:55 2003 ALGINVID 102
Wed Dec 17 14:58:55 2003 ARGS algoinvo 1
Wed Dec 17 14:58:55 2003 ARGS attrlist
external_database_id,nam
e,lowercase_name
Wed Dec 17 14:58:55 2003 ARGS comment
Wed Dec 17 14:58:55 2003 ARGS commit 1
Wed Dec 17 14:58:55 2003 ARGS debug
Wed Dec 17 14:58:55 2003 ARGS group
Wed Dec 17 14:58:55 2003 ARGS gusconfigfile
/home/apps/GUS/dev/.gus.
properties
Wed Dec 17 14:58:55 2003 ARGS project
Wed Dec 17 14:58:55 2003 ARGS refresh 1
Wed Dec 17 14:58:55 2003 ARGS sqlVerbose
Wed Dec 17 14:58:55 2003 ARGS tablename
SRes::ExternalDatabase
Wed Dec 17 14:58:55 2003 ARGS usage
Wed Dec 17 14:58:55 2003 ARGS user
Wed Dec 17 14:58:55 2003 ARGS valuelist 16^^^PfamA^^^pfama
Wed Dec 17 14:58:55 2003 ARGS verbose 1
Wed Dec 17 14:58:55 2003 ARGS veryVerbose
Wed Dec 17 14:58:55 2003 COMMIT commit on
Wed Dec 17 14:58:55 2003 Result primary key is found in database,
doing
update
name PfamA
lowercase_name pfama
Wed Dec 17 14:58:55 2003 RESULT
So, Now I am in doubt whether I am using the correct plugin(s).
Are there any plugins which does the database update job?Do I need to do
it at the SQL commandline.
Thanks
Sucheta
--
Sucheta Tripathy
Virginia Bioinformatics Institute
1880 pratt drive,Bldg XV
Virginia tech.
Blacksburg
Virginia
VA 24061
phone-(540)231-8138
|
|
From: Chris S. <sto...@pc...> - 2003-12-17 12:58:00
|
John does state that these are for DoTS: >> Summary: Two new tables to support motif rejection >> We need two new tables in the DoTS schema to support >> marking a motif as a bad motif. I think they do belong in DoTS because these are sequence annotation that we have generated for our purposes. As Joan indicated, I think your idea for programmatically helping her identify these is a good one, but the calls would still need to be reviewed and a place is still needed to store those calls. Chris On Dec 16, 2003, at 4:20 PM, Angel Pizarro wrote: > John, > In the table defs you don't state what schema space you are slating > for these tables. I will assume that you mean DoTS. > > It is debatable whether this is the proper place for these tables. > Here are my reasons: > > 1) Prodom is an external resource that we are mirroring and we do not > want to know anything about their algorithms for identifying motifs, > we want to import them whole-sale. This is slightly different that > saying we are rejecting a prodom motif. (e.g. It is still a valid > prodom motif, although not a very informative one) > > 2) What you really want is to make quality assesment calls on the > motifs prior running some learning algorithm for GO assignements. Is > this application specific information? Genome annotation that is > useful for other folks? I do not know. GUSDEVers, please pipe in here. > Unless it is useful for folks to have this information tied to the > motif itself, I would place these tables on some application specific > space. > > If there is utility to a qualtiy assement for imported motifs, then we > should also track "good" quality motifs, etc, not just rejected or > misleading motifs. Information content algorithms come to mind... > > Angel > > John Iodice wrote: > >> >> GUS folks, >> >> I'm working on the GO term predictor, which uses BLAST similarities >> between proteins of known function and domains from CDD or ProDom to >> automatically assign functions to novel proteins. This system is >> built around rules, which are domain - GO-term pairs. In some >> cases, bad, repeat-rich domains have given rise to bad rules. We >> want to create the ability to mark these domains so they are not used >> for the generation or application of rules (and possibly other >> functions unrelated to the GO term predictor). >> >> We propose to do this by means of two new tables. A motif will be >> marked as rejected by its addition to the rejectedMotif table. It >> will be identified by a source_id/external_database_id pair. The >> record will also include, for documentation, an >> external_database_release_id and a motif_rejection_reason_id. The >> latter will be the primary key of the motifRejectionReason table, >> which will store a name and description for each reason. >> >> The request is number 854957. Here's a link. I include the text >> below: >> https://sourceforge.net/tracker/? >> func=detail&aid=854957&group_id=54213&atid=479181 >> <https://sourceforge.net/tracker/? >> func=detail&aid=854957&group_id=54213&atid=479181> >> >> Thanks in advance for any comments. >> John >> >> ---------------------------------------------------------------------- >> ---------------------------------------------------------------------- >> ------------------------------------- >> >> Summary: Two new tables to support motif rejection >> We need two new tables in the DoTS schema to support >> marking a motif as a bad motif. They look like this: >> >> rejectedMotif >> ( >> rejected_motif_id number(10) not null, >> source_id varchar2(32) not null, >> external_database_id number(10) not null, >> external_database_release_id number(10) not null, >> motif_rejection_reason_id number(10) not null, >> {plus housekeeping columns} >> ) >> >> motifRejectionReason >> ( >> motif_rejection_reason_id number(10) not null, >> name varchar2(255) not null, >> description varchar2(255), >> {plus housekeeping columns} >> ) >> >> rejectedMotif should have an index on (source_id, >> external_database_id). >> >> rejectedMotif rows will number in the hundreds at most >> for the forseeable future. There will likely never be more >> than 20 rows in motifRejectionReason. > > > > ------------------------------------------------------- > 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 > |
|
From: Angel P. <an...@pc...> - 2003-12-16 21:20:44
|
John, In the table defs you don't state what schema space you are slating for these tables. I will assume that you mean DoTS. It is debatable whether this is the proper place for these tables. Here are my reasons: 1) Prodom is an external resource that we are mirroring and we do not want to know anything about their algorithms for identifying motifs, we want to import them whole-sale. This is slightly different that saying we are rejecting a prodom motif. (e.g. It is still a valid prodom motif, although not a very informative one) 2) What you really want is to make quality assesment calls on the motifs prior running some learning algorithm for GO assignements. Is this application specific information? Genome annotation that is useful for other folks? I do not know. GUSDEVers, please pipe in here. Unless it is useful for folks to have this information tied to the motif itself, I would place these tables on some application specific space. If there is utility to a qualtiy assement for imported motifs, then we should also track "good" quality motifs, etc, not just rejected or misleading motifs. Information content algorithms come to mind... Angel John Iodice wrote: > > GUS folks, > > I'm working on the GO term predictor, which uses BLAST similarities > between proteins of known function and domains from CDD or ProDom to > automatically assign functions to novel proteins. This system is > built around rules, which are domain - GO-term pairs. In some cases, > bad, repeat-rich domains have given rise to bad rules. We want to > create the ability to mark these domains so they are not used for the > generation or application of rules (and possibly other functions > unrelated to the GO term predictor). > > We propose to do this by means of two new tables. A motif will be > marked as rejected by its addition to the rejectedMotif table. It > will be identified by a source_id/external_database_id pair. The > record will also include, for documentation, an > external_database_release_id and a motif_rejection_reason_id. The > latter will be the primary key of the motifRejectionReason table, > which will store a name and description for each reason. > > The request is number 854957. Here's a link. I include the text below: > https://sourceforge.net/tracker/?func=detail&aid=854957&group_id=54213&atid=479181 > <https://sourceforge.net/tracker/?func=detail&aid=854957&group_id=54213&atid=479181> > > > Thanks in advance for any comments. > John > > --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- > > Summary: Two new tables to support motif rejection > > We need two new tables in the DoTS schema to support > marking a motif as a bad motif. They look like this: > > rejectedMotif > ( > rejected_motif_id number(10) not null, > source_id varchar2(32) not null, > external_database_id number(10) not null, > external_database_release_id number(10) not null, > motif_rejection_reason_id number(10) not null, > {plus housekeeping columns} > ) > > motifRejectionReason > ( > motif_rejection_reason_id number(10) not null, > name varchar2(255) not null, > description varchar2(255), > {plus housekeeping columns} > ) > > rejectedMotif should have an index on (source_id, > external_database_id). > > rejectedMotif rows will number in the hundreds at most > for the forseeable future. There will likely never be more > than 20 rows in motifRejectionReason. > |
|
From: John I. <io...@pc...> - 2003-12-16 18:40:43
|
GUS folks, I'm working on the GO term predictor, which uses BLAST similarities between proteins of known function and domains from CDD or ProDom to automatically assign functions to novel proteins. This system is built around rules, which are domain - GO-term pairs. In some cases, bad, repeat-rich domains have given rise to bad rules. We want to create the ability to mark these domains so they are not used for the generation or application of rules (and possibly other functions unrelated to the GO term predictor). We propose to do this by means of two new tables. A motif will be marked as rejected by its addition to the rejectedMotif table. It will be identified by a source_id/external_database_id pair. The record will also include, for documentation, an external_database_release_id and a motif_rejection_reason_id. The latter will be the primary key of the motifRejectionReason table, which will store a name and description for each reason. The request is number 854957. Here's a link. I include the text below: https://sourceforge.net/tracker/?func=detail&aid=854957&group_id=54213&a tid=479181 Thanks in advance for any comments. John ------------------------------------------------------------------------ ------------------------------------------------------------------------ --------------------------------- Summary: Two new tables to support motif rejection We need two new tables in the DoTS schema to support marking a motif as a bad motif. They look like this: rejectedMotif ( rejected_motif_id number(10) not null, source_id varchar2(32) not null, external_database_id number(10) not null, external_database_release_id number(10) not null, motif_rejection_reason_id number(10) not null, {plus housekeeping columns} ) motifRejectionReason ( motif_rejection_reason_id number(10) not null, name varchar2(255) not null, description varchar2(255), {plus housekeeping columns} ) rejectedMotif should have an index on (source_id, external_database_id). rejectedMotif rows will number in the hundreds at most for the forseeable future. There will likely never be more than 20 rows in motifRejectionReason. |
30 messages has been excluded from this view by a project administrator.
