From tiffany21dollars at hotmail.com Mon Mar 1 03:38:38 2004 From: tiffany21dollars at hotmail.com (monty) Date: Mon Mar 1 03:44:46 2004 Subject: [BioSQL-l] Su-per V 1 A-G R A Message-ID: <1078130318-25898@excite.com> Did you know That the normal cost for Super V i a g r a is $20, per dose? We are running a hot special!! T0DAY Its only an amazing $3.00 Shipped world wide! DISC0UNT 0RDER: http://healthypolicy.com/sv/index.php?pid=eph9106 kiss cuddlesquebec bmw buttons mookie gocougs dodgers electric ruxsugar olivier theking zhongguo wolverin nesbitt Get off this list by going to http://healthypolicy.com/sv/applepie.php From hlapp at gnf.org Mon Mar 1 14:57:51 2004 From: hlapp at gnf.org (Hilmar Lapp) Date: Mon Mar 1 15:03:44 2004 Subject: [BioSQL-l] Re: undef strand and biosql In-Reply-To: Message-ID: Hm. Strand being undef is a soft violation, in the sense that there is a value defined for 'unknown strand' (namely 0). Bottom line is that an undef strand should not lead to failure. I'll either fix bioperl-db to automatically substitute 0 for undef, or we could fix bioperl to return 0 if the strand hasn't been set yet. The latter is risky because then it is difficult to impossible to ask whether the strand has already been set but is unknown, or whether it's never been set and therefore you want to set a default. Any votes from the bioperl'ers out there on this question? I'm afraid my vote would go for not returning 0 by default in the location object. Actually, we could also put a DEFAULT 0 in the column definition in the schema DDL. That doesn't necessarily fix it in all RDBMSs though if you directly assign NULL to the column (e.g., in Oracle). Any votes on that from the biosql community? -hilmar On Monday, March 1, 2004, at 09:21 AM, matthieu CONTE wrote: > I solve the problem of 'source_term_id' by create -source_tag => > 'tigr'...and it seems to be ok...... > > "$seq->add_SeqFeature(new Bio::SeqFeature::Generic( > -primary => 'RIGHT_UTR', > -source_tag => 'tigr', > -start .......... > " > But it still have a problem of undef column 'strand' > Maybe in : > $loc->add_sub_Location(new Bio::Location::Simple( > -start => $e->{'start'}, > -end => $e->{'end'}, > -strand => ???? > )); > but I?m also confuse with the tag: ?strand? of Bio::SeqFeature::Generic > > I have this warning: > -------------------- WARNING --------------------- > MSG: insert in Bio::DB::BioSQL::LocationAdaptor (driver) failed, > values were ("1","318","","1") FKs (16957,) > Column 'strand' cannot be null > --------------------------------------------------- > Could not store 8356.t04040: > ------------- EXCEPTION ------------- > MSG: create: object (Bio::Location::Simple) failed to insert or to be > found by unique key > STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create > /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/DB/BioSQL/ > BasePersistenceAdaptor.pm:207 > STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store > /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/DB/BioSQL/ > BasePersistenceAdaptor.pm:253 > STACK Bio::DB::Persistent::PersistentObject::store > /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/DB/Persistent/ > PersistentObject.pm:270 > STACK Bio::DB::BioSQL::SeqFeatureAdaptor::store_children > /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/DB/BioSQL/ > SeqFeatureAdaptor.pm:278 > STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create > /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/DB/BioSQL/ > BasePersistenceAdaptor.pm:215 > STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store > /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/DB/BioSQL/ > BasePersistenceAdaptor.pm:253 > STACK Bio::DB::Persistent::PersistentObject::store > /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/DB/Persistent/ > PersistentObject.pm:270 > STACK Bio::DB::BioSQL::SeqAdaptor::store_children > /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/DB/BioSQL/ > SeqAdaptor.pm:246 > STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create > /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/DB/BioSQL/ > BasePersistenceAdaptor.pm:215 > STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store > /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/DB/BioSQL/ > BasePersistenceAdaptor.pm:253 > STACK Bio::DB::Persistent::PersistentObject::store > /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/DB/Persistent/ > PersistentObject.pm:270 > STACK (eval) load_seqdatabase.pl:517 > STACK toplevel load_seqdatabase.pl:500 > > > > > ----------------------------------------------------------- > Matthieu CONTE > M. Sc. in Bioinformatics from SIB > > CIRAD-Biotrop TA40/03 > Avenue Agropolis > 34398 Montpellier Cedex 5 > FRANCE > > m_conte@hotmail.com > tel: (33)04 67 61 60 21 > fax :(33) 4 67 61 56 05 > > ----------------------------------------------------------- > > > > > >> From: Hilmar Lapp >> To: Josh Lauricha >> CC: "matthieu CONTE" , bioperl-l@bioperl.org >> Subject: Re: [Bioperl-l] Re: Bio ::seqIO ::tigr >> Date: Fri, 27 Feb 2004 16:45:13 -0800 >> >> >> On Thursday, February 26, 2004, at 09:45 AM, Josh Lauricha wrote: >> >>> Does the source_term_id refer to the source_tag()? >> >> Yes. >> >>> >>> On Feb 26, 2004, at 9:08 AM, matthieu CONTE wrote: >>> >>>> [conte@bearn biosql]$ perl load_seqdatabase.pl --dbuser biosql >>>> --dbpass biosql --namespace orysa_tigr --format tigr >>>> /home/conte/pipeline_orthologues/data/orysa_tigr/chr07.xml >>>> Loading /home/conte/pipeline_orthologues/data/orysa_tigr/chr07.xml >>>> ... >>>> >>>> -------------------- WARNING --------------------- >>>> MSG: insert in Bio::DB::BioSQL::SeqFeatureAdaptor (driver) failed, >>>> values were ("","1") FKs (26216,37,) >>>> Column 'source_term_id' cannot be null >>>> --------------------------------------------------- >>>> >> >> What this means is that there was no $feat->source_tag set, and >> looking up undef resulted in undef for the foreign key :-) >> >> While bioperl doesn't enforce it, for biosql the source_tag() as well >> as the primary_tag() of a feature are mandatory and cannot be undef. >> Most SeqIO parsers set source_tag() to a static default if there is >> no value, e.g. 'EMBL/GenBank/SwissProt' if you're using FTHelper.pm. >> >> -hilmar >> -- >> ------------------------------------------------------------- >> Hilmar Lapp email: lapp at gnf.org >> GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 >> ------------------------------------------------------------- >> >> > > _________________________________________________________________ > MSN Messenger : discutez en direct avec vos amis ! > http://www.msn.fr/msger/default.asp > > -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From electric21godzilla at hotmail.com Wed Mar 3 22:37:05 2004 From: electric21godzilla at hotmail.com (terrence) Date: Wed Mar 3 22:42:55 2004 Subject: [BioSQL-l] Su-per V 1 A-G R A Message-ID: <1078371425-12595@excite.com> Did you know That the normal cost for Super V i a g r a is $20, per dose? 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  • qwerty musengo tjyeon hector detroit fierro Skidoo christopulos texas serodnic arcimo saints tardis rwengert adam deshan ryan Get off this list by writing to getmeoff731@excitemail.com From rbauer at informatik.hu-berlin.de Tue Mar 9 04:07:09 2004 From: rbauer at informatik.hu-berlin.de (Raphael A. Bauer) Date: Tue Mar 9 04:12:33 2004 Subject: [BioSQL-l] KW field from Swiss-Prot in Biosql schema missing Message-ID: <404D893D.7060902@informatik.hu-berlin.de> > It becomes a tag/value annotation represented in biosql by bioentry_qualifier_value. The referenced term should be 'keyword', > and the value will be the actual keyword. > You'll have one row per keyword. > That's not the case in my biosql Schema. Only the GN (Gene Name) Lines from Swiss-Prot are parsed into Bioentry_qualifier_value. The KW Field is still missing. Raphael From hlapp at gnf.org Tue Mar 9 14:16:17 2004 From: hlapp at gnf.org (Hilmar Lapp) Date: Tue Mar 9 14:21:58 2004 Subject: [BioSQL-l] KW field from Swiss-Prot in Biosql schema missing In-Reply-To: <404D893D.7060902@informatik.hu-berlin.de> Message-ID: <3D3DDC92-71FE-11D8-A93D-000A959EB4C4@gnf.org> On Tuesday, March 9, 2004, at 01:07 AM, Raphael A. Bauer wrote: > That's not the case in my biosql Schema. Only the GN (Gene Name) Lines > from Swiss-Prot are parsed into Bioentry_qualifier_value. > The KW Field is still missing. > You will need at least the latest stable release of bioperl, which is 1.4.x The 1.2 series stores the keyword in a way that will not get persisted by bioperl-db. To verify, read in a swissprot-formatted sequence with keywords and then print the 'keyword'-tagged annotations: $seqio = Bio::SeqIO->new(-format => "swiss", -file => ">myswissprot.dat"); $seq = $seqio->next_seq(); foreach my $kw ($seq->annotation->get_Annotations("keyword")) { print "KW: ",$kw->value,"\n"; } This should print you all keywords that the sequence had in the input file. The trick about serializing keywords to biosql is that there is no trick. Bio::Seq::RichSeq (instances of which are returned by the swissprot parser) stores keywords as Bio::Annotation::SimpleValue objects behind the scenes (since 1.4.x), and bioperl-db just serializes all annotation objects. With bioperl 1.2 this will not work because that one stores keywords in a separate property. -hilmar -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From binky21guinness at hotmail.com Tue Mar 16 23:44:27 2004 From: binky21guinness at hotmail.com (rodrigo) Date: Tue Mar 16 10:48:54 2004 Subject: [BioSQL-l] The Hot New Drug that puts V-1-A-G-R-A to shame! Message-ID: <1079498667-6863@excite.com> The Biggest New Drug since V1agra! Many times as powerful. http://pro-meds.net/sv/index.php?pid=eph9106 -A quicker more stable erection -More enjoyable sex for both -Longer sex -Known to add length to you erection -Lasts up to 36 hours (not a thrity-six hour erection, but enhancement for thirty-six) We have it at a discounted savings. Save when you go through our site on all your orders. http://pro-meds.net/sv/index.php?pid=eph9106 vanilla safetyledzep wolverin bobcat t-bone kenneth marcus liverpoo praiseladdie reynolds fiona advil minou norman Get off this list go to http://suzuki.pro-meds.net/sv/index.php?pid=eph9106 From len at reeltwo.com Wed Mar 17 15:58:28 2004 From: len at reeltwo.com (Len Trigg) Date: Wed Mar 17 16:04:15 2004 Subject: [BioSQL-l] Re: [Biojava-dev] Re: biosql In-Reply-To: References: <4055CB2F.8060303@yahoo.co.uk> <4055CEB3.1060809@yahoo.co.uk> Message-ID: Thomas Down wrote: > On 15 Mar 2004, at 15:41, Matthew Pocock wrote: > > Scratch that - a clean rebuild seems to have fixed it. I am getting a > > single failure though: > > > > Testcase: testFeaturePersistence took 0.843 sec > > FAILED > > [feature] location is now an instance of: > > org.biojava.bio.symbol.RangeLocation > > No it isn't -- I've been waiting for this failure to be fixed before > turning on the database-dependent tests. Trouble is, we don't make a > nightly release if *any* tests fail, and this one has been hanging > around for a while... This is one of the two BioJava/BioSQL bugs found a few weeks ago by Frederik Decouttere. I fixed the other one but haven't had a chance to deal to this one. The problem is that when a BetweenLocation (and probably a whole bunch of others) get persisted, they get retrieved as regular RangeLocations. It would be straight forward to store a term corresponding to the location type in the term_id of the location table (currently unused in our binding). It's just a matter of determining what terms to use. Either (easiest to hardest): a) the classname of the location type; b) whatever BioPerl uses (if it is capable of persisting the location type); c) jump through a few hoops and look up an appropriate obda name. Has anyone ever tried testing whether sequences of any complexity written to BioSQL via the BioJava binding are readable via BioPerl, and vice versa? I believe our Ontology persistence has currently diverged from the BioSQL schema somewhat anyway. Cheers, Len. From hlapp at gnf.org Thu Mar 18 15:22:35 2004 From: hlapp at gnf.org (Hilmar Lapp) Date: Thu Mar 18 15:28:03 2004 Subject: [BioSQL-l] Re: [Biojava-dev] Re: biosql In-Reply-To: Message-ID: On Wednesday, March 17, 2004, at 12:58 PM, Len Trigg wrote: > The problem is that when a BetweenLocation (and probably a whole bunch > of others) get persisted, they get retrieved as regular > RangeLocations. It would be straight forward to store a term > corresponding to the location type in the term_id of the location > table (currently unused in our binding). This is what I proposed this foreign key for. > It's just a matter of determining what terms to use. Either (easiest > to hardest): a) the > classname of the location type; b) whatever BioPerl uses (if it is > capable of persisting the location type); c) jump through a few hoops > and look up an appropriate obda name. Please don't use classnames, although that would be easiest obviously, or otherwise bioperl (or any other language) won't interoperate with this properly. As a matter of fact, bioperl-db doesn't use this currently, and therefore doesn't support fuzzy locations (which is what we call them in bioperl) to roundtrip to fuzzy locations (they'll become exact locations). Note also that generally speaking the location_qualifier_value table is supposed to hold information from which you could infer the type of location. My point at the time was that querying location_qualifier_value every single time you obtain a location regardless of type is going to be a huge waste of time, given that 99% of locations are *not* fuzzy. -hilmar -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From ev1anduncan at hotmail.com Mon Mar 22 16:41:57 2004 From: ev1anduncan at hotmail.com (sydney) Date: Mon Mar 22 16:47:19 2004 Subject: [BioSQL-l] Order PR0ZAC with no questions! 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So far, I have distributed money to some charity organizations in the U.A.E, Algeria and Malaysia. Now that my health has deteriorated so badly, I cannot do this myself anymore. I once asked members of my family to close one of my accounts and distribute the money which I have there to charity organization in Bulgaria and Pakistan, they refused and kept the money to themselves. Hence, I do not trust them anymore, as they seem not to be contended with what I have left for them. The last of my money which no one knows of is the huge cash deposit of eighteen million dollars $18,000,000,00 that I have with a finance/Security Company abroad. I will want you to help me collect this deposit and dispatched it to charity organizations. I have set aside 10% for you and for your time. God be with you. 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