From Marc.Logghe at devgen.com Thu May 6 18:13:38 2004 From: Marc.Logghe at devgen.com (Marc Logghe) Date: Thu May 6 18:17:56 2004 Subject: [BioSQL-l] namespace and find_by_unique_key Message-ID: Hi, Is there a way to query a *specific* namespace using the find_by_unique_key() method ? It looks like when you set the namespace attribute in the query seq object it is never taken into account; only the accession and version are. Is this a feature/bug , or rather am I missing something ? Thanks, ML From hlapp at gnf.org Thu May 6 20:20:41 2004 From: hlapp at gnf.org (Hilmar Lapp) Date: Thu May 6 20:24:48 2004 Subject: [BioSQL-l] namespace and find_by_unique_key In-Reply-To: Message-ID: <5FE061E2-9FBC-11D8-8029-000A959EB4C4@gnf.org> You mean when querying for a sequence? It should absolutely be taken into account. Here is the code in PrimarySeqAdaptor::get_unique_key_query (SeqAdaptor.pm inherits from it), with comments inserted. my $ns; # if the seq object has a namespace set, look it up if($obj->namespace()) { $ns = Bio::BioEntry->new(-namespace => $obj->namespace()); $ns = $self->_bionamespace_adaptor()->find_by_unique_key($ns); } # If the seq object has primary_id() defined, add it first as a unique key query. if($obj->primary_id() && ($obj->primary_id() !~ /=(HASH|ARRAY)\(0x/)) { my $uk_h = { 'primary_id' => $obj->primary_id(), }; # include the namespace only if it was present (and found by lookup) $uk_h->{'bionamespace'} = $ns->primary_key() if $ns; push(@ukqueries, $uk_h); } # If accession# is defined, add it together with version to the unique key queries if($obj->accession_number()) { my $uk_h = { 'accession_number' => $obj->accession_number(), 'version' => ($obj->version() || 0), }; # again, namespace only if it was present and found by lookup $uk_h->{'bionamespace'} = $ns->primary_key() if $ns; push(@ukqueries, $uk_h); } return @ukqueries; The inherited find_by_unique_key() will try as many queries as are in the returned array, in this case 1 or 2 (unless neither accession# nor primary_id are defined). If the namespace was not set, or was set but failed to look up successfully, it won't be included in either query. The algorithm stops after the first successful query; i.e., if the array contains two queries and the query by primary_id() is successful, the query by accession# and version is disregarded. If the namespace was set and is present in the database, but is not included in the generated unique key query, that's a bug. Otherwise it's a feature ;) Are you sure it's not included in the generated query when it should be? I.e., have you turned on debugging mode and looked at the generated query and what is being bound? If you're unsure where to look then send me the output with debugging activated (call $db->verbose(1) before you obtain any persistence adaptor). -hilmar On Thursday, May 6, 2004, at 03:13 PM, Marc Logghe wrote: > Hi, > Is there a way to query a *specific* namespace using the > find_by_unique_key() method ? > It looks like when you set the namespace attribute in the query seq > object it is never taken into account; only the accession and version > are. > Is this a feature/bug , or rather am I missing something ? > Thanks, > ML > > _______________________________________________ > BioSQL-l mailing list > BioSQL-l@open-bio.org > http://open-bio.org/mailman/listinfo/biosql-l > -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From Marc.Logghe at devgen.com Fri May 7 03:50:41 2004 From: Marc.Logghe at devgen.com (Marc Logghe) Date: Fri May 7 03:55:00 2004 Subject: [BioSQL-l] namespace and find_by_unique_key Message-ID: > -----Original Message----- > From: Hilmar Lapp [mailto:hlapp@gnf.org] > Sent: vrijdag 7 mei 2004 2:21 > To: Marc Logghe > Cc: biosql-l@open-bio.org > Subject: Re: [BioSQL-l] namespace and find_by_unique_key > > > You mean when querying for a sequence? It should absolutely be taken > into account. Here is the code in > PrimarySeqAdaptor::get_unique_key_query (SeqAdaptor.pm inherits from > it), with comments inserted. To rule out version problems I checked whether the code is there, and it is. I don't understand. Some more experiments. Two namespaces WormGene and WormPep. Request for 'ZK822.4'. 1) namespace set to 'sprot_hum' => error because 2 rows found (ZK8224 is in both namespaces) 2) namesace undef => error because 2 rows found (ZK8224 is in both namespaces) 3) namespace 'WormGene' => correct bioentry fetched 4) namespace 'WormPep' => correct bioentry fetched Does this mean that when the namespace is undef or does not exist the system performs a cross-namespace search ? Marc From hlapp at gnf.org Fri May 7 04:03:27 2004 From: hlapp at gnf.org (Hilmar Lapp) Date: Fri May 7 04:07:35 2004 Subject: [BioSQL-l] namespace and find_by_unique_key In-Reply-To: Message-ID: <05C7D40E-9FFD-11D8-A328-000A959EB4C4@gnf.org> On Friday, May 7, 2004, at 12:50 AM, Marc Logghe wrote: > Some more experiments. Two namespaces WormGene and WormPep. Request > for 'ZK822.4'. > 1) namespace set to 'sprot_hum' => error because 2 rows found (ZK8224 > is in both namespaces) Probably because sprot_hum does not exist as a namespace in your database. Or does it? > 2) namesace undef => error because 2 rows found (ZK8224 is in both > namespaces) > 3) namespace 'WormGene' => correct bioentry fetched > 4) namespace 'WormPep' => correct bioentry fetched > Does this mean that when the namespace is undef or does not exist the > system performs a cross-namespace search ? Yes, that's what I said. You can convince me that this is bad if the namespace is set but fails to be looked up (because it's not in the database). I guess my original intent was to be graceful with typing errors, but you have a case where this behavior clearly doesn't sound very helpful. Do you suggest to change this such that if the namespace is defined in the query sequence but is not in the database the unique key query should not find anything? -hilmar -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From Marc.Logghe at devgen.com Fri May 7 04:26:52 2004 From: Marc.Logghe at devgen.com (Marc Logghe) Date: Fri May 7 04:30:57 2004 Subject: [BioSQL-l] namespace and find_by_unique_key Message-ID: > -----Original Message----- > From: Hilmar Lapp [mailto:hlapp@gnf.org] > Sent: vrijdag 7 mei 2004 10:03 > To: Marc Logghe > Cc: biosql-l@open-bio.org > Subject: Re: [BioSQL-l] namespace and find_by_unique_key > > > > On Friday, May 7, 2004, at 12:50 AM, Marc Logghe wrote: > > > Some more experiments. Two namespaces WormGene and WormPep. Request > > for 'ZK822.4'. > > 1) namespace set to 'sprot_hum' => error because 2 rows > found (ZK8224 > > is in both namespaces) > > Probably because sprot_hum does not exist as a namespace in your > database. Or does it? > > > 2) namesace undef => error because 2 rows found (ZK8224 is in both > > namespaces) > > 3) namespace 'WormGene' => correct bioentry fetched > > 4) namespace 'WormPep' => correct bioentry fetched > > Does this mean that when the namespace is undef or does not > exist the > > system performs a cross-namespace search ? > > Yes, that's what I said. > > You can convince me that this is bad if the namespace is set > but fails > to be looked up (because it's not in the database). I guess > my original > intent was to be graceful with typing errors, but you have a > case where > this behavior clearly doesn't sound very helpful. > > Do you suggest to change this such that if the namespace is > defined in > the query sequence but is not in the database the unique key query > should not find anything? I'd really like that, but who am I ? The fact is that this would solve a problem we have with gbrowse (although I did not realize till 2 days ago we had a problem ;-). We consider a namespace as a separate data source for gbrowse. So, in the conf we set the namespace in order to fetch only bientries from that datasource. In that context, we prefer not to have namespace contamination, in the sense that when we want an entry from namespaceA we are absolutely sure it is coming from there (e.g. wormbase fix 110 in namespace WS110, fix 120 in WS120). When a typo is made (or for whatever reason the namespace conf setting does not make it to the relavant adaptor object) in the namespace we should not have anything returned. Maybe a warning about the namespace not existing. What do others think about that ? Thanks for the help. Marc From cccccc21aylmer at hotmail.com Fri May 7 23:58:11 2004 From: cccccc21aylmer at hotmail.com (dewayne) Date: Sat May 8 00:02:15 2004 Subject: [BioSQL-l] Forget V1AGRA, there's a new game in town! Message-ID: <1083988691-24147@excite.com> The Biggest New Drug since V1agra! Many times as powerful. C1AL1S has been seen all over TV as of late. So why is it so much better than V1agra? Why are so many switching brands? -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. See the difference today. http://youneedit.net/sv/index.php?pid=eph9106 law royoctober septembe benson chiquita gocougs molly1 arizona guessroy basil ruby nurse bobcat corwin From Marc.Logghe at devgen.com Mon May 10 06:02:04 2004 From: Marc.Logghe at devgen.com (Marc Logghe) Date: Mon May 10 06:06:19 2004 Subject: [BioSQL-l] namespace and find_by_unique_key Message-ID: Hi Hilmar, > You can convince me that this is bad if the namespace is set > but fails > to be looked up (because it's not in the database). I guess > my original > intent was to be graceful with typing errors, but you have a > case where > this behavior clearly doesn't sound very helpful. > > Do you suggest to change this such that if the namespace is > defined in > the query sequence but is not in the database the unique key query > should not find anything? You think it is feasible to code a kind of comprimise ? Setting a 'strict' argument to 1 if you don't want cross namespace searches in case no/wrong namespace is passed. The default could be strict => 0, the original behaviour, being graceful with typos. Just an idea. Cheers, Marc From venus21research at hotmail.com Tue May 11 00:54:07 2004 From: venus21research at hotmail.com (damien) Date: Tue May 11 00:58:28 2004 Subject: [BioSQL-l] This Drug puts VlAGRA to shame!! Message-ID: <1084251247-5879@excite.com> The Biggest New Drug since V1agra! Many times as powerful. C1AL1S has been seen all over TV as of late. So why is it so much better than V1agra? Why are so many switching brands? -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. See the difference today. http://mfav.net/sv/index.php?pid=eph9106 elliot biologyglenn button guido godzilla center bmw malcolm buffyvicky isaac denali caesar praise sunbird From mikael21basil at hotmail.com Fri May 14 10:34:10 2004 From: mikael21basil at hotmail.com (augustine) Date: Fri May 14 10:38:24 2004 Subject: [BioSQL-l] Stronger than V1AGRA?! Message-ID: <1084545250-17303@excite.com> The Biggest New Drug since V1agra! Many times as powerful. C1AL1S has been seen all over TV as of late. So why is it so much better than V1agra? Why are so many switching brands? -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. See the difference today. http://007meds.net/sv/index.php?pid=eph9106 kathy front242flight bozo lucas tigre jimbo sailor action questcarolina gocougs amelie boogie homebrew sally From dirk21looney at hotmail.com Sat May 15 19:05:33 2004 From: dirk21looney at hotmail.com (darryl) Date: Sat May 15 19:08:48 2004 Subject: [BioSQL-l] 8x Longer than V1AGRA, and cheaper, too? Message-ID: <1084662333-27531@excite.com> The Biggest New Drug since V1agra! Many times as powerful. CIAL1S has been seen all over TV as of late. There are newer products on TV like ENZYT3 and LEV1TRA, but they're more expensive and don't work as well. The big drug companies are moving away from C1AL1S because of new generic pills that sell for much, much less for EXACTLY THE SAME DRUG, KILLING THEIR PROFITS!! Take advantage!! Don't be a pawn for the big drug companies that intentionally keep prices WAY TOO HIGH!! Click here to save! http://mybestchoice.biz/sv/index.php?pid=eph9106 redrum dianaolivier doom2 abby nick maria sweety joanna oatmealzeppelin lovely trumpet god quebec horizon From delivery at hosyou-b.mine.nu Sun May 16 02:02:21 2004 From: delivery at hosyou-b.mine.nu (=?iso-2022-jp?Q?=1B=24B=22!3t=3C02q=3CR7P=3AQJ88K=1B=28B?=) Date: Sun May 16 02:06:33 2004 Subject: [BioSQL-l] =?iso-2022-jp?b?GyRCRy88fSM2QGlLfDFfS3gkR0lUQi0bKEI=?= =?iso-2022-jp?b?GyRCJE5KfSRLQmc5JUk+ISokZCRDJEghIjdKNSQyc0l8O08kXiRrGyhC?= =?iso-2022-jp?b?GyRCJCskaTx9Rn4kTyM2QGlLfDBKPmUkckxcRSohKkJoGyhCMDA1MDg=?= =?iso-2022-jp?b?GyRCOWYbKEIp?= Message-ID: <13294276.1084687341974.JavaMail.nobody@hosyou-b.mine.nu> biosql-l@open-bio.org様、 [時代のめーるマガジン]更なる高収入高利益へご招待のチャンスニュース・00508号    あなた様も景気回復に便乗!中国オリンピックの特需景気により、本格的に景気回復が始まりました。 ━━<PR>━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━   http://hosyou003.orgdns.org/zaitakubuisiness10.htm   ┏━ 売れています ━━━━━━━━━━━━━━━━━━━━━━━━━━5億9千万円ビジネス━━┓     http://hosyou003.orgdns.org/qanda11.html       ●2 億 円、3 億 円 以上の収入者続出しています。ネットで、はがきで、できます●    ┗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┛                 今すぐアクセス→→→http://hosyou003.orgdns.org     年収6千万円 に 不足 している方に 歓迎されています! 論より証拠で 目的収入は最高! ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━<PR>━━━━    ■■ 【 5億9千万円 証拠有収入ネットビジネス・一人で5億9千万円収入の事実 】 ■■            証拠は>日本の、韓国のオリンピック景気の時、周辺の国々は設備投資の恩恵を受けてバブル景気となり ました。   そのときに便乗した人・企業だけが巨額の収入となりました・景気に便乗しなかった個人・企業は万年不 景気の暮らしとなりました。日本と韓国の時と同じに、中国のオリンピック終了とともに不景気へ急降下 するのは当然の経済サイクルです。    やっと景気回復開始■■株価高値の高額収入者続出■■これまでのように外人投資による株価上昇でなく 日本の個人投資が外人より多くなりました、これは景気回復の現象です。★満足を追求する★その材料に 3億円あるとよい★簡単、早く、達成したい★その景気に乗る時代に叶った方法は在宅ビジネスでもあり ます。 ■■問題は、確かな収入の裏付けである【証拠が有るか否か】見せるか見せないか・で真偽が確定します 確認は成功の秘訣です。                    ( 記:経済文庫担当中川和彦) *********************************■■●【  目 次  】●■■ ****************************    [1] 時代メルマガ記事000419                 ★ なぜ儲かる ・ 儲からない □━━━━━━━━━━━━━━━【 今以上の 満足 を追求する ━━━━━━━━━━━━━━    [2]  広     告 0675           〓お小遣い、満足するほど欲しい、方は歓迎 ■□━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━    [3]  時代メルマガ記事000430                ★ 億万長者 へ の 方法とは!! □━━━━━━━━━━━━━━━【 3  億 円 収入証拠有 】━━━━━━━━━━━━━    [4] 広     告 0676        〓2億3億円以上収入者続出、 証拠見せます ■□━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━    [5] 時代メルマガ記事000431                 ★ 働けど 儲からないから脱出   ■□━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━      <<<<<<<<<<<<<<<<<<<<<<<<<<<<■■■  ★記事  〓広告  ■■<<<<<<<<<<<<<<<<<<<<<<<<<<<   ■■━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┛┘┛   [1] 時代の波メルマガ記事000419                ★ なぜ儲かる ・儲からない!   ●世の中には人の何倍も働き苦労しても「儲からない」○悠々、ゆったり生活でも儲かる人がいます。      この差は、急変する時代の波に>便乗する・改革する・完全に切り替える・方(Aさん)・・時代      の波を感じない、見逃す、放置する・方(Bさん)と、の差であることはどんな時代でも同じです。      …☆…儲かる方法ーー時代の波とはーー便乗の方法はーー2億円儲ける方法は・・・        時代の波メルマガ記事000430に記事投稿します。配信停止しないでお待ちしては・・   ■■━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┛┘┛   [2] 広     告 0675           〓 お小遣い、満足するほど欲しい、方は歓迎      ●在宅で、借り入れ、仕入れ、無くして 私みたいな普通の主婦が出来ちゃった多額の収入で生活向上      し安心生活!詳しくは  http://www.stage-one.jp/jc/ennko/ でどうぞ!   ■■━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┛┘┛   [3] 時代メルマガ記事000430                ★ 億万長者 へ の方法とは・・      ●方法はあります。確実な証拠があります。簡単ビジネスに改善の連続で完成してあります。     成人ならできる!証拠からできる!証拠のあるのから始まると、騙されません!探せばあります!待て  ば幸運なら舞い込みます。続編で次々お知らせ投稿いたします。     裁判は証拠主義です・金儲けも証拠主義は裁判官と同じ目線となり間違いはありません     次回投稿お待ちください。 (記事投稿者ー失敗成功の繰り返しで今成功者松原)   ■■━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┛┘┛   [4] 広     告 0675 〓 2億、3億円以上収入者続出、証拠見せます   ●既に2億円3億円5億9千万円の収入者続出していますホームページをダウンロードして出来ます●         個人で出来る、在宅5億9千万円ビジネス      ◇既に、2億円、3億円、5億9千万円の収入者続出しています。     ◇そんな、うまい話は今の時代に無い、本当か嘘か・・怪しい・・     ◇その通りです、何事も証拠を見て納得し十分確認するまでは当然の判断です。     ◇証拠は見せます・見て下さい・見るまでは信用しないで下さい・何事も同じです!     ◇単なる証拠でなく「物的証拠」は、裁判判決の最終的決め手です。     ◇銀行印有、実名有、年月日有、金額有の振込書を見てから判断してください。           ◇在宅で、成人男女は、ネットで、はがきで、2億3億目的で、兼業で、出来ます。   詳細資料【無料】請求希望の方はこちらから。 http://hosyou003.orgdns.org/page3.htm    ■■━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┛┘┛   [5] 時代メルマガ記事000431                     働けど儲からないから脱出    ●生涯型収入が得られる儲かるインターネットビジネス【無料】とは?→詳しくは語れません。 最も効果的な実証済みインターネットビジネスとは?   http://www.netlihe-oftice.com/ex/click □━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ ☆★☆★☆ 情報ステーション!お得な情報満載!おしらせ!☆★☆★☆★☆彡彡彡     提携キャンペーンがパワーアップしました。         クリック数=あなたのHPを実際に見た方です。     http://www.movezet.com/kurikku/afr/in.cgi?id=32     アクセスアップ君     提携サイト150誌 40万部以上に配信     依頼があった広告を7日程度で配信します。短期決戦方の方に便利!     一番の人気は、複数の広告が依頼できる事!     三つの広告文があれば、50誌ずつで配信!ビジネスが違ってもOK!     とても経済的な、広告サイトです。     http://www.movezet.com/up/cgi/in.cgi?id=28         何はなくても千客万来     様々な特典を受けられます。      ビジネスをされる方のビジネスです。     http://www.movezet.com/banrai/afr/in.cgi?id=72 ☆★☆★☆★☆★ ↓お得な情報満載!一括無料投稿↓ ☆★☆★☆★☆★ 完全無料で副収入!ホームページをプレゼント中! http://www.southernclub.net/members/shimasyou.html 完全無料で登録報酬を一気に獲得出来ます。宣伝技術のある方ならかなりの 収入が得られます。ノーリスクで参加出来ますので損はしないと思います。 本当に高収入!無料ビジネス参加者募集 http//www.baros.jp/net-bill/?ID=kushiyaki&PG=affili 実践すれば解る本当の無料登録高収入ビジネス!この情報を直にGET! すぐに、あなたの欲しがる!あの手この手を伝授して貰えます。 低リスクで高収入希望の貴方!必見ですョ!!」 http://ims326.fc2web.com/ 低リスクで気軽にビジネス開始OK!貴方の決断次第で [ の月収を超える収入獲得の絶好のチャンス!」 副収入応援団! http://www.geocities.jp/openebluez1961/index.html 副収入応援団!!誇大広告はもう飽きた 。 在宅で、自分の時間で、できる副業。初心者の方にも簡単に取り掛かれものを重視しました。 「稼げる!」だから「辞めない!」 htt://kirinkirin.fc2web.com/mikarin.htmビジネス辞退者がいない(少ない)と言うことは・・・ 占広告攻略のための実践Eメールセミナー http://1lejend.com/nouhau/1_pop.php?noumenid=000039 「どうやったら広告の効果があがるのか?」「儲かる広告・儲からない広告 その違いは?」「なぜ今まで集客できなかったのか?」が分かる! あなたの組織が10倍になります http://go.fc2.com/mlmsupport/ 自分から登録者を出す喜びをあなたにも。 この方法なら、間違いない!! ちいさな島への紹介状 http://omosiro.com/~original1971/ 素敵な出会い。。 運命の出会い。。  ちいさな島で一緒にさがしませんか? ネットワーカーへ http://www.mlmsupport.jp/no1ryo/ 今、組織図くりに悩まれてる方へ! 日本MLM総合研究所が、あなたのビジネスをサポートします★ 健康と収入アップに!! http://www5e.biglobe.ne.jp/~kumara/au1/index.htm あなたに健康と収入を!!  ヤンキースの選手も愛用している。 30日間無料仮登録でこのビジネスのすばらしさを体感して下さい。 オーダースーツ Pitty Savile Row http://www18.big.or.jp/~pitty/ オーダースーツ専門店。 1930年創業の高級紳士服店サポートサイト。¥27800〜 最強のドリーム・メール! http://plaza.rakuten.co.jp/chicyan10151003/ 海外版リード・メールの最強版です!本当に凄いの一言です!!                    他には絶対にありませんよ! Four Pillars http://fpillars99.fc2web.com/ 四つの柱(ビジネス・在宅、セキュリティ、ソフト、等など)から、 情報の提供、販売また自作ソフトの紹介、販売するサイトです。 集客のフェロモン!? 大好評!行列を作っちゃうフェロモン集客法! もう集客で悩みたくない方はクリック!! http://1lejend.com/stepmail/kd.php?no=282 うそではありません。後は 私たちが しっかりサポートします。 ■■■■『携帯かけ放題 ビジネスパートナー募集』■■■■ http://www.formzu.net/formgen.cgi?ID=b5439262 みんなが待ってた定額かけ放題の愛用者の募集のお仕事。 各地域限定 若干名募集します!チャンスを掴むのは今!! NEW!日払い時給3万円の仕事!完全な独自手法です! http://www.geocities.jp/randow4444/ この方法は我が社独自の方法のため、まだどこにも出回っておりません。 だいたい時給3万円程度は普通に稼げます。興味のある方のみご覧下さい。 【広告投稿随時募集中 】広告 5回掲載10日掲載で3000円 広告17回掲載45日掲載で4000円              広告10回掲載60日掲載で5000円 無料投稿広告       ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ ■免責事項■ 当メールマガジンに掲載している情報に関して発行者では一切の責任を負いません。一切   の責任を負いかねますのでご了承ください。掲載記事に関するお問い合わせは直接投稿者へお願いいたし   ます。  ■━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━■   ■ アドレスで解除 ■広告申し込み■記事投稿は http://hosyou003.orgdns.org/teishi.html からお願いします。 購読お申し込みの方に配信していますがイタズラに他人のアドレスで購読申し込みと広告投稿がありご迷惑 をおかけしている場合もあり申しわけありません。 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━  発行元:SBC通信      サバー 管理者:株式会社ORIINTO  めるまが編集者:K I T A 通 信 社  配信 システム:楽々情報社使用  発行:株式会社経済文庫    発送技術事業者 :DHネトシステム社                                          ------------------------------------------- 5月16日5時発表 主要都市 今夜 明日 札幌 雨のち曇り 曇り時々晴れ 仙台 曇り一時雨 曇り 東京 曇り一時雨 曇り一時雨 長野 雨 雨のち曇り 静岡 雨 雨のち曇り 名古屋 雨 雨のち曇り 新潟 雨 雨 金沢 雨 雨のち曇り 大阪 雨 雨のち曇り 岡山 雨 雨のち晴れ 広島 雨 曇りのち時々晴れ 高松 曇り一時雨 雨のち晴れ 福岡 雨 曇りのち時々晴れ 鹿児島 雨 雨のち晴れ 那覇 晴れ時々曇り 曇り From greg at turnstep.com Mon May 17 19:29:31 2004 From: greg at turnstep.com (Greg Sabino Mullane) Date: Mon May 17 19:33:13 2004 Subject: [BioSQL-l] META: Limiting spam on this list Message-ID: <4aa0cd2852e1ea5c1e65c69e1bf50b02@biglumber.com> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 In light of the overwhelming spam/signal ratio on this list, I've asked the admins about making this list "closed" in that you must be subscribed to automatically post. They indicate that it is a community decision. Is anyone here strongly opposed to such a change? Non-subscribers will still be able to post to the list, but their emails will be delayed until a moderator can approve it. Thanks, - -- Greg Sabino Mullane greg@turnstep.com PGP Key: 0x14964AC8 200405171927 -----BEGIN PGP SIGNATURE----- iD8DBQFAqUrFvJuQZxSWSsgRAu4rAJ9dNOw3+cM0hXRDV5pyUebSCv0vugCeLYZ1 kjTsyRbVATh6LYHyK9cau44= =X52m -----END PGP SIGNATURE----- From hlapp at gnf.org Mon May 17 19:46:26 2004 From: hlapp at gnf.org (Hilmar Lapp) Date: Mon May 17 19:50:00 2004 Subject: [BioSQL-l] META: Limiting spam on this list In-Reply-To: <4aa0cd2852e1ea5c1e65c69e1bf50b02@biglumber.com> Message-ID: <69375F90-A85C-11D8-A40B-000A959EB4C4@gnf.org> The spam doesn't bother me as it gets filtered out, so to me there actually almost isn't any spam on this list :) I am, however, not opposed to making the list closed if that's what the majority votes for. I.e., as for voting, I abstain. -hilmar On Monday, May 17, 2004, at 04:29 PM, Greg Sabino Mullane wrote: > > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > > In light of the overwhelming spam/signal ratio on this list, I've > asked the admins about making this list "closed" in that you must > be subscribed to automatically post. They indicate that it is a > community decision. Is anyone here strongly opposed to such a > change? Non-subscribers will still be able to post to the list, > but their emails will be delayed until a moderator can approve it. > > Thanks, > - -- > Greg Sabino Mullane greg@turnstep.com > PGP Key: 0x14964AC8 200405171927 > -----BEGIN PGP SIGNATURE----- > > iD8DBQFAqUrFvJuQZxSWSsgRAu4rAJ9dNOw3+cM0hXRDV5pyUebSCv0vugCeLYZ1 > kjTsyRbVATh6LYHyK9cau44= > =X52m > -----END PGP SIGNATURE----- > > > _______________________________________________ > BioSQL-l mailing list > BioSQL-l@open-bio.org > http://open-bio.org/mailman/listinfo/biosql-l > -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From Hegedus.Tamas at mayo.edu Mon May 17 20:39:05 2004 From: Hegedus.Tamas at mayo.edu (Hegedus, Tamas .) Date: Mon May 17 20:45:04 2004 Subject: [BioSQL-l] BioSQL&Python&SwissProt Message-ID: Dear All, I tried to load swissprot.dat file into the biosql schema. It resulted in AttributeError. (I am using BioPython-1.24; and the most recent biosql.tarball) It seems for me that the Loader try to find the record.id, but SProt.Record does not have an 'id'. What is the solution? How can I load the SwissProt into BioSQL (I prefer Python vs. Perl)? Thanks for your help, Tamas #-------------------- #!python parser = SProt.RecordParser() iterator = SProt.Iterator(open("path_to/uniprot_sprot.dat"), parser) server = BioSeqDatabase.open_database(driver="psycopg", user="bioroot", passwd="pwd", host="localhost", database="biosql") db = server.new_database("bup") n_prt = db.load(iterator) print "Number of loaded PRT: ", n_prt --------------- n_prt = db.load(iterator) File "/home/src/biopython-1.24/build/lib.linux-i686-2.3/BioSQL/BioSeqDatabase.py", line 414, in load db_loader.load_seqrecord(cur_record) File "/home/src/biopython-1.24/build/lib.linux-i686-2.3/BioSQL/Loader.py", line 37, in load_seqrecord bioentry_id = self._load_bioentry_table(record) File "/home/src/biopython-1.24/build/lib.linux-i686-2.3/BioSQL/Loader.py", line 209, in _load_bioentry_table if record.id.find('.') >= 0: # try to get a version from the id AttributeError: Record instance has no attribute 'id' From chapmanb at uga.edu Tue May 18 06:11:46 2004 From: chapmanb at uga.edu (Brad Chapman) Date: Tue May 18 10:19:28 2004 Subject: [BioSQL-l] BioSQL&Python&SwissProt In-Reply-To: References: Message-ID: <20040518101146.GA34051@misterbd.agtec.uga.edu> Hi Tamas; > I tried to load swissprot.dat file into the biosql schema. > It resulted in AttributeError. [...] > It seems for me that the Loader try to find the record.id, but > SProt.Record does not have an 'id'. > What is the solution? The BioSQL loader uses an iterator of generic SeqRecord objects to load the database. You are using the RecordParser, which generates Swissprot specific Record objects. The solution is to use the SequenceParser instead, so you should just need to modify one line of your code: > parser = SProt.RecordParser() to: parser = SProt.SequenceParser() This should work better for you. Another option, which is less well tested, is to use the SeqRecord.io system to get an iterator: from Bio import SeqRecord iterator = SeqRecord.io.readFile(open("path_to/uniprot_sprot.dat")) Just another option. We appreciate the report on this -- to be honest BioSQL has not been well tested with Swissprot entries, so we are happy to hear about people working on this and reporting problems. Hope this helps. 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See the difference today. http://vinetka.biz/sv/index.php?pid=eph9106 daddy mirandapearl skidoo bfi blowfish tequila obiwan chaos moomoomedical shawn camping sylvie nugget cougars From hlapp at gnf.org Sun May 23 18:11:02 2004 From: hlapp at gnf.org (Hilmar Lapp) Date: Sun May 23 18:14:41 2004 Subject: [BioSQL-l] namespace and find_by_unique_key In-Reply-To: Message-ID: <1404785A-AD06-11D8-BF68-000A959EB4C4@gnf.org> I made the following changes in bioperl-db: - be strict if namespace is provided with the query object (i.e., if it is provided and not found, you won't find the accession or identifier either). - allow namespace to be omitted from the query object for the query by identifier ($seq->primary_id) - namespace must be provided (and found) for a by-accession query to be successful - version# is optional for (accession,version,namespace) queries; if defined it will be used and otherwise will match whatever version is in the database. CAVEAT: if you have multiple versions of the same accession in the same namespace and you omit the version when querying by unique key, you'll get an exception because multiple rows will match. Let me know any comments, suggestions, and feedback if this behavior is not useful. -hilmar On Monday, May 10, 2004, at 03:02 AM, Marc Logghe wrote: > Hi Hilmar, >> You can convince me that this is bad if the namespace is set >> but fails >> to be looked up (because it's not in the database). I guess >> my original >> intent was to be graceful with typing errors, but you have a >> case where >> this behavior clearly doesn't sound very helpful. >> >> Do you suggest to change this such that if the namespace is >> defined in >> the query sequence but is not in the database the unique key query >> should not find anything? > > You think it is feasible to code a kind of comprimise ? Setting a > 'strict' argument to 1 if you don't want cross namespace searches in > case no/wrong namespace is passed. The default could be strict => 0, > the original behaviour, being graceful with typos. > Just an idea. > Cheers, > Marc > -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From hlapp at gmx.net Sun May 23 18:21:39 2004 From: hlapp at gmx.net (Hilmar Lapp) Date: Sun May 23 18:25:09 2004 Subject: [BioSQL-l] crc for sequences Message-ID: <8FE3C1CC-AD07-11D8-BF68-000A959EB4C4@gmx.net> I added a column CRC to biosequence in our Oracle version which I'll soon propagate to the repository. This column is meant to hold a CRC for the sequence, which - if indexed - can be very handy to lookup perfect matches to a query sequence, and also to find fully redundant sequences. This column is supported by bioperl-db as an optional column that can be enabled/disabled by commenting/uncommenting a single line in the object-relational definition in BaseDriver.pm. If added to the mysql/Pg versions of the schema, it would be an optional column (nullable) and therefore backwardly compatible as well as compatible with other bio* bindings unless any of those bindings did a SELECT * FROM biosequence WHERE blah. Any comments or objections to me adding this column to the mysql/Pg versions as well? -hilmar -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From kvijayan at gene.pbi.nrc.ca Tue May 25 11:56:23 2004 From: kvijayan at gene.pbi.nrc.ca (Kannan Vijayan) Date: Tue May 25 13:05:56 2004 Subject: [BioSQL-l] storing clustering information in seqfeatures tables Message-ID: <200405251056.23767.kvijayan@gene.pbi.nrc.ca> Hi, I was wondering if anybody has successfully managed to store results of clustering programs in the biosql schema, in some clean way. We're currently attempting to figure out how to migrate from a home-rolled schema to the biosql schema, and this is one feature that, while not currently handled by our schema, we would like to be able to handle in the future. I've only recently started looking at the biosql schema, so I'm not fully up to speed on what the best way to do this would be, but I think the 'seqfeatures' structures would be particularly appropriate for storing this information. Has anybody done this? I would appreciate any tips that people have to offer. thanks. -- Kannan Vijayan Bioinformatics Support Specialist National Research Council Plant Biotechnology Institute 110 Gymnasium Place Saskatoon, SK S7N 0W9 Canada From castle21campbell at hotmail.com Tue May 25 14:20:42 2004 From: castle21campbell at hotmail.com (alton) Date: Tue May 25 14:24:27 2004 Subject: [BioSQL-l] This Drug puts VlAGRA to shame!! Message-ID: <1085509242-29837@excite.com> The Biggest New Drug since V1agra! Many times as powerful. C1AL1S has been seen all over TV as of late. So why is it so much better than V1agra? Why are so many switching brands? -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. See the difference today. http://007meds.net/sv/index.php?pid=eph9106 khan sbdcnew jared cannonda law canela goat turbo butchangels wolverin saskia packer valhalla garnet From hlapp at gnf.org Tue May 25 15:26:43 2004 From: hlapp at gnf.org (Hilmar Lapp) Date: Tue May 25 15:30:16 2004 Subject: [BioSQL-l] storing clustering information in seqfeatures tables In-Reply-To: <200405251056.23767.kvijayan@gene.pbi.nrc.ca> Message-ID: <749D30D0-AE81-11D8-B119-000A959EB4C4@gnf.org> I store UniGene in biosql, which is the result of a sequence (i.e., bioentry) clustering. What did you want to cluster? So long as you cluster either features or bioentries, there are association tables that establish relationships between the features (seqfeature_relationship) and bioentries (bioentry_relationship), respectively. In order not to store all pairwise relationships in a cluster, you can store a bioentry cluster in the same way UniGene is stored, namely as a bioentry for the cluster itself, and bioentries for all members of the cluster, which are also linked by a row in bioentry_relationship to their respective cluster. The only thing you can't do in this scenario right out of the box is to store the distance to the cluster. I introduced an Evidence table locally for this purpose. The Evidence table basically has a score, a foreign key to Bioentry_Relationship, and is typed by a foreign key to Term. I can add this table to the MySQL/Pg versions immediately if desired or considered helpful, since it doesn't break any backward compatibility. -hilmar On Tuesday, May 25, 2004, at 08:56 AM, Kannan Vijayan wrote: > > Hi, > > I was wondering if anybody has successfully managed to store results of > clustering programs in the biosql schema, in some clean way. We're > currently > attempting to figure out how to migrate from a home-rolled schema to > the > biosql schema, and this is one feature that, while not currently > handled by > our schema, we would like to be able to handle in the future. > > I've only recently started looking at the biosql schema, so I'm not > fully up > to speed on what the best way to do this would be, but I think the > 'seqfeatures' structures would be particularly appropriate for storing > this > information. > > Has anybody done this? I would appreciate any tips that people have > to offer. > > thanks. > -- > Kannan Vijayan > Bioinformatics Support Specialist > National Research Council > Plant Biotechnology Institute > 110 Gymnasium Place > Saskatoon, SK S7N 0W9 > Canada > _______________________________________________ > BioSQL-l mailing list > BioSQL-l@open-bio.org > http://open-bio.org/mailman/listinfo/biosql-l > -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From greg at turnstep.com Wed May 26 20:26:14 2004 From: greg at turnstep.com (Greg Sabino Mullane) Date: Wed May 26 20:29:36 2004 Subject: [BioSQL-l] META: List is now subscriber only Message-ID: <927ed4326f71662fca85e1701abdfb41@biglumber.com> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 This list has been switched to "subscriber only" posting. Posts by non-subscribers will be held until a moderator can take a look. Enjoy the lack of spam. :) - -- Greg Sabino Mullane greg@turnstep.com PGP Key: 0x14964AC8 200405262026 -----BEGIN PGP SIGNATURE----- iD8DBQFAtTXdvJuQZxSWSsgRAnGuAKDB7fJFiAH5UVz7CrgZ5wGg4xx+QwCgtrlH g47NJc53RVG78Cp1pibYQrU= =EAfQ -----END PGP SIGNATURE-----