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[Gusdev-gusdev] Re: LoadPfam doubts
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From: Terry C. <tw...@cs...> - 2003-12-24 06:35:03
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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 . |
