From hauswedell@mi.fu-berlin.de Fri Aug 07 19:37:27 2009 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1MZTNe-0003JD-8M>; Fri, 07 Aug 2009 19:37:26 +0200 Received: from einhorn.in-berlin.de ([192.109.42.8]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1MZTNe-0007Mn-6X>; Fri, 07 Aug 2009 19:37:26 +0200 X-Envelope-From: hauswedell@mi.fu-berlin.de X-Envelope-To: Received: from fbsdlap.freedom.lan (86-40-105-249-dynamic.b-ras2.mvw.galway.eircom.net [86.40.105.249]) (authenticated bits=0) by einhorn.in-berlin.de (8.13.6/8.13.6/Debian-1) with ESMTP id n77HbOeZ006056 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT) for ; Fri, 7 Aug 2009 19:37:25 +0200 From: Hannes Hauswedell To: seqan-dev@lists.fu-berlin.de Date: Fri, 7 Aug 2009 19:37:14 +0200 User-Agent: KMail/1.11.4 (FreeBSD/7.2-PRERELEASE; KDE/4.2.4; i386; ; ) MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Message-Id: <200908071937.14999.hauswedell@mi.fu-berlin.de> X-Scanned-By: MIMEDefang_at_IN-Berlin_e.V. on 192.109.42.8 X-Originating-IP: 192.109.42.8 X-purgate: clean X-purgate-ID: 151147::1249666646-0000691A-F221A895/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.1.6 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Kenia.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=0.1 required=5.0 tests=FORGED_RCVD_HELO Subject: [Seqan-dev] =?iso-8859-1?q?=DCbersetzung_DNA=285=29_-=3E_AA?= X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 Precedence: list List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Fri, 07 Aug 2009 17:37:27 -0000 Hallo *, ich arbeite gerade am BLASTX-Modus f=FCr RazerBlastS, meinem BA-Projekt.=20 Dazu muss ich einen DNA-String in einen Aminos=E4ure-String konvertieren. Ich hatte gehofft, das platzsparend durch einen Funktor realisieren zu=20 k=F6nnen, der DNA[3] in AminoAcid[1] =FCbersetzt. Dann k=F6nnte ich sogar=20 einfach zwei Suffixe der Quelle reinstecken und h=E4tte alle drei Reading- =46rames ohne mehr Platz abgedeckt.=20 Leider gestaltet sich das etwa schwieriger als gedacht, ModView<>=20 scheint nur f=FCr char2char-Translations geeignet. Ob ModifiedString<>=20 =FCberhaupt daf=FCr zu gebrauchen ist, konnte ich bis jetzt noch nicht=20 rausfinden. Kann mir da jemand weiterhelfen? Ich hab schon diverses versucht, brauch=20 aber als Ergebnis unbedingt etwas, was sich auch ansonsten wie ein=20 String verh=E4lt :/ Vielen Dank f=FCr Ihre/eure Hilfe, Hannes P.S: Ich habe auch relativ lange in der Doku gesucht, weil ich=20 eigentlich dachte, Seqan m=FCsste sowas haben. Ist Translation nicht etwas= =20 oft benutztes? From hauswedell@mi.fu-berlin.de Tue Aug 18 01:08:36 2009 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1MdBJb-00059U-BG>; Tue, 18 Aug 2009 01:08:35 +0200 Received: from einhorn.in-berlin.de ([192.109.42.8]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1MdBJb-0000NF-9O>; Tue, 18 Aug 2009 01:08:35 +0200 X-Envelope-From: hauswedell@mi.fu-berlin.de Received: from fbsdlap.freedom.lan (soulrebel.in-vpn.de [217.197.85.84]) (authenticated bits=0) by einhorn.in-berlin.de (8.13.6/8.13.6/Debian-1) with ESMTP id n7HN8XxI005768 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT); Tue, 18 Aug 2009 01:08:34 +0200 From: Hannes Hauswedell To: David Weese Date: Tue, 18 Aug 2009 01:08:32 +0200 User-Agent: KMail/1.12.0 (FreeBSD/7.2-PRERELEASE; KDE/4.3.0; i386; ; ) MIME-Version: 1.0 Content-Type: Text/Plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Message-Id: <200908180108.33076.hauswedell@mi.fu-berlin.de> X-Scanned-By: MIMEDefang_at_IN-Berlin_e.V. on 192.109.42.8 X-Originating-IP: 192.109.42.8 X-purgate: clean X-purgate-ID: 151147::1250550515-000059FE-585DF6B1/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.1.6 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Togo.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=0.1 required=5.0 tests=FORGED_RCVD_HELO Cc: seqan-dev@lists.fu-berlin.de Subject: [Seqan-dev] Lokales Banded-Alignment X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 Precedence: list List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Mon, 17 Aug 2009 23:08:36 -0000 Hallo David und andere, ich versuche bei mir ein lokales Banded-Alignment mit Gotoh zu machen.=20 Daf=FCr benutzte ich bis jetzt: TScoreValue myScore =3D globalAlignment(result_frags, pairSet, options.blastScoring, AlignConfig(), diagLow, diagHigh, BandedGotoh() ); Das Problem hierbei ist, das auch mit dieser AlignConfig, das Max nur in=20 letzter Zeile und Spalte, nicht aber "mittendrin" gesucht wird (die=20 =46unktion ist schlie=DFlich "globalAlignment"). Ich k=F6nnte nat=FCrlich von Beginn des ersten Fragments bis zum Ende des=20 letzten nochmal global scoren, aber das ist ein extra Aufruf, der das=20 Gesamte noch weiter bremst (dieser Funktionsaufruf ist jetzt schon der=20 Bottleneck). localAlignment() kann ich daf=FCr nicht verwenden, weil das kein Gotoh und= =20 erst Recht kein BandedGotoh unterst=FCtzt. Was kann man da tun? K=E4me ich im Nachhinein noch an den Score an der=20 Stelle x,y in der DP-Matrix dran? x,y w=E4re hierbei das Ende des letzten=20 =46ragments (bzw. wegen reverser Orientierung, des ersten). Vielen Dank, Hannes From Tobias.Rausch@fu-berlin.de Tue Aug 18 09:46:44 2009 Received: from outpost1.zedat.fu-berlin.de ([130.133.4.66]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1MdJP0-00038c-Pr>; Tue, 18 Aug 2009 09:46:42 +0200 Received: from relay2.zedat.fu-berlin.de ([130.133.4.80]) by outpost1.zedat.fu-berlin.de (Exim 4.69) with esmtp (envelope-from ) id <1MdJP0-0006oh-OJ>; Tue, 18 Aug 2009 09:46:42 +0200 Received: from exchange6.fu-berlin.de ([160.45.9.133]) by relay2.zedat.fu-berlin.de (Exim 4.69) with esmtp (envelope-from ) id <1MdJP0-0005M6-Km>; Tue, 18 Aug 2009 09:46:42 +0200 Received: from exchange6.fu-berlin.de ([160.45.9.133]) by exchange6.fu-berlin.de ([160.45.9.133]) with mapi; Tue, 18 Aug 2009 09:46:42 +0200 From: "Rausch, Tobias" To: 'Hannes Hauswedell' , 'David Weese' Date: Tue, 18 Aug 2009 09:46:41 +0200 Thread-Topic: [Seqan-dev] Lokales Banded-Alignment Thread-Index: Acofj6gh7LzVZNaDRyW2G94gvyrJDAARrLeQ Message-ID: <6AB91D0276C1E744892C72E49C9DFFF7376A48985C@exchange6.fu-berlin.de> References: <200908180108.33076.hauswedell@mi.fu-berlin.de> In-Reply-To: <200908180108.33076.hauswedell@mi.fu-berlin.de> Accept-Language: en-US, de-DE Content-Language: de-DE X-MS-Has-Attach: X-MS-TNEF-Correlator: acceptlanguage: en-US, de-DE Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 X-Originating-IP: 160.45.9.133 X-purgate: clean X-purgate-ID: 151147::1250581602-000059FE-96BEA855/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.001460, version=1.1.6 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Kongo.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED X-Mailman-Approved-At: Tue, 18 Aug 2009 10:37:35 +0200 Cc: "'seqan-dev@lists.fu-berlin.de'" Subject: Re: [Seqan-dev] Lokales Banded-Alignment X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 Precedence: list List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Tue, 18 Aug 2009 07:46:44 -0000 Hallo Hannes, > K=E4me ich im Nachhinein noch an den Score an der Stelle x,y in der DP-Ma= trix dran?=20 Leider nein, Gotoh, BandedGotoh & Co. speichern alle immer nur eine Spalte = bei der Berechnung um Memory zu sparen. > localAlignment() kann ich daf=FCr nicht verwenden, weil das kein Gotoh un= d erst Recht kein BandedGotoh unterst=FCtzt. Der SmithWaterman hinter dem localAlignment() verwendet lineare Gapkosten i= st also ein "Gotoh-Style" Algorithmus. Was in der Tat noch fehlt in SeqAn ist ein BandedSmithWaterman. > Das Problem hierbei ist, das auch mit dieser AlignConfig, das=20 > Max nur in letzter Zeile und Spalte, nicht aber "mittendrin"=20 > gesucht wird (die Funktion ist schlie=DFlich "globalAlignment"). Ja stimmt, was du vermutlich brauchst ist der BandedSmithWaterman und den g= ibt es leider noch nicht, sorry. David kennt deine Aufgabe besser, insofern hat der vielleicht noch eine Ide= e dazu. Gr=FC=DFe, Tobias > -----Urspr=FCngliche Nachricht----- > Von: seqan-dev-bounces@lists.fu-berlin.de=20 > [mailto:seqan-dev-bounces@lists.fu-berlin.de] Im Auftrag von=20 > Hannes Hauswedell > Gesendet: Tuesday, August 18, 2009 1:09 AM > An: David Weese > Cc: seqan-dev@lists.fu-berlin.de > Betreff: [Seqan-dev] Lokales Banded-Alignment >=20 > Hallo David und andere, >=20 > ich versuche bei mir ein lokales Banded-Alignment mit Gotoh=20 > zu machen.=20 > Daf=FCr benutzte ich bis jetzt: >=20 > TScoreValue myScore =3D globalAlignment(result_frags, pairSet, > options.blastScoring, > =20 > AlignConfig(), > diagLow, diagHigh, > BandedGotoh() ); >=20 > Das Problem hierbei ist, das auch mit dieser AlignConfig, das=20 > Max nur in letzter Zeile und Spalte, nicht aber "mittendrin"=20 > gesucht wird (die Funktion ist schlie=DFlich "globalAlignment"). > Ich k=F6nnte nat=FCrlich von Beginn des ersten Fragments bis zum=20 > Ende des letzten nochmal global scoren, aber das ist ein=20 > extra Aufruf, der das Gesamte noch weiter bremst (dieser=20 > Funktionsaufruf ist jetzt schon der Bottleneck). >=20 > localAlignment() kann ich daf=FCr nicht verwenden, weil das=20 > kein Gotoh und erst Recht kein BandedGotoh unterst=FCtzt. >=20 > Was kann man da tun? K=E4me ich im Nachhinein noch an den Score=20 > an der Stelle x,y in der DP-Matrix dran? x,y w=E4re hierbei das=20 > Ende des letzten Fragments (bzw. wegen reverser Orientierung,=20 > des ersten). >=20 > Vielen Dank, > Hannes >=20 > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev > = From hauswedell@mi.fu-berlin.de Tue Aug 18 17:05:49 2009 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1MdQFw-00085G-2X>; Tue, 18 Aug 2009 17:05:48 +0200 Received: from einhorn.in-berlin.de ([192.109.42.8]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1MdQFw-0002hz-0c>; Tue, 18 Aug 2009 17:05:48 +0200 X-Envelope-From: hauswedell@mi.fu-berlin.de Received: from fbsdlap.freedom.lan (soulrebel.in-vpn.de [217.197.85.84]) (authenticated bits=0) by einhorn.in-berlin.de (8.13.6/8.13.6/Debian-1) with ESMTP id n7IF5kqH027801 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT); Tue, 18 Aug 2009 17:05:47 +0200 From: Hannes Hauswedell To: "Rausch, Tobias" Date: Tue, 18 Aug 2009 17:05:44 +0200 User-Agent: KMail/1.12.0 (FreeBSD/7.2-PRERELEASE; KDE/4.3.0; i386; ; ) References: <200908180108.33076.hauswedell@mi.fu-berlin.de> <6AB91D0276C1E744892C72E49C9DFFF7376A48985C@exchange6.fu-berlin.de> In-Reply-To: <6AB91D0276C1E744892C72E49C9DFFF7376A48985C@exchange6.fu-berlin.de> MIME-Version: 1.0 Content-Type: Text/Plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Message-Id: <200908181705.44960.hauswedell@mi.fu-berlin.de> X-Scanned-By: MIMEDefang_at_IN-Berlin_e.V. on 192.109.42.8 X-Originating-IP: 192.109.42.8 X-purgate: clean X-purgate-ID: 151147::1250607948-000059FE-ED09DF1C/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.1.6 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Togo.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=0.1 required=5.0 tests=FORGED_RCVD_HELO Cc: "'seqan-dev@lists.fu-berlin.de'" , 'David Weese' Subject: Re: [Seqan-dev] Lokales Banded-Alignment X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 Precedence: list List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Tue, 18 Aug 2009 15:05:49 -0000 Hallo Tobias, danke f=FCr die schnelle Antwort! Am Dienstag, 18. August 2009 09:46:41 schrieb Rausch, Tobias: > Hallo Hannes, > > > K=E4me ich im Nachhinein noch an den Score an der Stelle x,y in der > > DP-Matrix dran? > > Leider nein, Gotoh, BandedGotoh & Co. speichern alle immer nur eine > Spalte bei der Berechnung um Memory zu sparen. Hm, macht Sinn. > > localAlignment() kann ich daf=FCr nicht verwenden, weil das kein > > Gotoh und erst Recht kein BandedGotoh unterst=FCtzt. > > Der SmithWaterman hinter dem localAlignment() verwendet lineare > Gapkosten ist also ein "Gotoh-Style" Algorithmus. Da kann ich auch andere gapOpen, als gapExtend-Kosten angeben? > Was in der Tat noch > fehlt in SeqAn ist ein BandedSmithWaterman. > > > Das Problem hierbei ist, das auch mit dieser AlignConfig, das > > Max nur in letzter Zeile und Spalte, nicht aber "mittendrin" > > gesucht wird (die Funktion ist schlie=DFlich "globalAlignment"). > > Ja stimmt, was du vermutlich brauchst ist der BandedSmithWaterman und > den gibt es leider noch nicht, sorry. Obwohl ein lokales Banded ja auch nicht so sinnvoll ist, wie ein=20 (semi-)globales Banded, da bei einem wirklich lokalen Alignment die=20 Wahrscheinlichtkeit ja auch nicht h=F6her ist im Band / in Entfernung k um= =20 die Hauptdiagonale zu sein, als irgendwo anders. Insofern ist das=20 Problem vielleicht viel tiefer und die Frage ob wir wirklich on lokales=20 Alignment wollen, und wenn ja, dass wir es dann anders realisieren=20 m=FCssen. Aber da kann mir nur David weiterhelfen, denke ich. Bez=FCglich dem globalAlignment und der R=FCckgabe von Fragmenten habe ich= =20 aber noch einige Verst=E4ndnissprobleme. David meinte die Fragmente seien=20 die exakten St=FCcke des Alignments, so dass ich vor dem ersten Fragment=20 und nach dem letzten "abschneiden" kann um "lokaler" zu werden. In der=20 Realit=E4t bekomme ich aber ganz andere "unlokale" Ergebnisse, z.B: Query: 0 AGCCATTAGAGGCCACCACACCAGACG 27 ||||||||||||||||||||||| =20 Sbjct: 214 GGCCATTAGAGGCCACCACACCAG--- 238 Die Fragmentinformationen: =46RAGMENT 0: read begin: 26 geno begin: 237 length: 1 =46RAGMENT 1: read begin: 0 geno begin: 214 length: 23 Woher kommt da das 0te Fragment, und wieso beginnt das erste mit einem=20 Mismatch? (Hier ist der Read vollst=E4ndig also semiglobal aliniert) Ein anderer Hit ist wiederum tats=E4chlicher lokaler, endet jedoch auch=20 mit einem MisMatch: Query: 6 CCATTAGAGGCCACCACACCG 27 ||||||||||||||||||||=20 Sbjct: 216 CCATTAGAGGCCACCACACCA 237 Unabh=E4ngig von den Fragmenten, bezieht sich der Score auch auf das echte= =20 globale Alignment, weicht also von dem hier gezeigten stark ab. Das w=E4re ein weiterer Grund warum das Verfahren ungeeignet ist, wobei=20 ich nat=FCrlich Alignments die den Read nicht vollst=E4ndig enthalten ein=20 zweites Mal scoren k=F6nnte (was im Endeffekt - wie erw=E4hnt - dann aber=20 wahrscheinlich den Geschwindigkeitsvorteil vom Banded kaputt macht). Danke f=FCr die Hilfe, Gru=DF, Hannes > > > -----Urspr=FCngliche Nachricht----- > > Von: seqan-dev-bounces@lists.fu-berlin.de > > [mailto:seqan-dev-bounces@lists.fu-berlin.de] Im Auftrag von > > Hannes Hauswedell > > Gesendet: Tuesday, August 18, 2009 1:09 AM > > An: David Weese > > Cc: seqan-dev@lists.fu-berlin.de > > Betreff: [Seqan-dev] Lokales Banded-Alignment > > > > Hallo David und andere, > > > > ich versuche bei mir ein lokales Banded-Alignment mit Gotoh > > zu machen. > > Daf=FCr benutzte ich bis jetzt: > > > > TScoreValue myScore =3D globalAlignment(result_frags, pairSet, > > options.blastScoring, > > > > AlignConfig(), > > diagLow, diagHigh, > > BandedGotoh() ); > > > > Das Problem hierbei ist, das auch mit dieser AlignConfig, das > > Max nur in letzter Zeile und Spalte, nicht aber "mittendrin" > > gesucht wird (die Funktion ist schlie=DFlich "globalAlignment"). > > Ich k=F6nnte nat=FCrlich von Beginn des ersten Fragments bis zum > > Ende des letzten nochmal global scoren, aber das ist ein > > extra Aufruf, der das Gesamte noch weiter bremst (dieser > > Funktionsaufruf ist jetzt schon der Bottleneck). > > > > localAlignment() kann ich daf=FCr nicht verwenden, weil das > > kein Gotoh und erst Recht kein BandedGotoh unterst=FCtzt. > > > > Was kann man da tun? K=E4me ich im Nachhinein noch an den Score > > an der Stelle x,y in der DP-Matrix dran? x,y w=E4re hierbei das > > Ende des letzten Fragments (bzw. wegen reverser Orientierung, > > des ersten). > > > > Vielen Dank, > > Hannes > > > > _______________________________________________ > > seqan-dev mailing list > > seqan-dev@lists.fu-berlin.de > > https://lists.fu-berlin.de/listinfo/seqan-dev =2D-=20 Solidarische Gr=FC=DFe Hannes From Tobias.Rausch@fu-berlin.de Tue Aug 18 17:37:15 2009 Received: from outpost1.zedat.fu-berlin.de ([130.133.4.66]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1MdQkM-0000cn-R4>; Tue, 18 Aug 2009 17:37:14 +0200 Received: from relay2.zedat.fu-berlin.de ([130.133.4.80]) by outpost1.zedat.fu-berlin.de (Exim 4.69) with esmtp (envelope-from ) id <1MdQkM-0005hh-PX>; Tue, 18 Aug 2009 17:37:14 +0200 Received: from exchange6.fu-berlin.de ([160.45.9.133]) by relay2.zedat.fu-berlin.de (Exim 4.69) with esmtp (envelope-from ) id <1MdQkM-0006ej-Lm>; Tue, 18 Aug 2009 17:37:14 +0200 Received: from exchange6.fu-berlin.de ([160.45.9.133]) by exchange6.fu-berlin.de ([160.45.9.133]) with mapi; Tue, 18 Aug 2009 17:37:14 +0200 From: "Rausch, Tobias" To: 'Hannes Hauswedell' Date: Tue, 18 Aug 2009 17:37:14 +0200 Thread-Topic: [Seqan-dev] Lokales Banded-Alignment Thread-Index: AcogFWCY5bmESNOVTpSwT1haiYSIoQAAUMUA Message-ID: <6AB91D0276C1E744892C72E49C9DFFF7376A4898AA@exchange6.fu-berlin.de> References: <200908180108.33076.hauswedell@mi.fu-berlin.de> <6AB91D0276C1E744892C72E49C9DFFF7376A48985C@exchange6.fu-berlin.de> <200908181705.44960.hauswedell@mi.fu-berlin.de> In-Reply-To: <200908181705.44960.hauswedell@mi.fu-berlin.de> Accept-Language: en-US, de-DE Content-Language: de-DE X-MS-Has-Attach: X-MS-TNEF-Correlator: acceptlanguage: en-US, de-DE Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 X-Originating-IP: 160.45.9.133 X-purgate: clean X-purgate-ID: 151147::1250609834-000059FE-6BFB6B77/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000001, version=1.1.6 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Kenia.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED Cc: 'David, "'seqan-dev@lists.fu-berlin.de'" , Weese' Subject: Re: [Seqan-dev] Lokales Banded-Alignment X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 Precedence: list List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Tue, 18 Aug 2009 15:37:16 -0000 Hallo Hannes, > Da kann ich auch andere gapOpen, als gapExtend-Kosten angeben? Ja. > Obwohl ein lokales Banded ja auch nicht so sinnvoll ist, wie=20 > ein (semi-)globales Banded.... Also wenn du den kompletten Read in einem Ausschnitt vom Genom finden wills= t (semi-global), dann geht das mit dem AlignConfig. Setze das genom als 1. string und den read als 2. und nehme AlignConfig. > David meinte=20 > die Fragmente seien die exakten St=FCcke des Alignments, so=20 > dass ich vor dem ersten Fragment und nach dem letzten=20 > "abschneiden" kann. Die Fragmente sind im Sinne der DP-Matrix alle Diagonalen, also Matches UND= Mismatches. Aufgrund des tracebacks kommen die Fragmente im=20 String > alle r=FCckw=E4rts. Ein einzelnes Fragment hat 5 members, die id des 1. strings, die begin posi= tion im 1. string, die id des 2. strings, die begin position im 2. string und die laenge des matches. Demnach ist > Query: 0 AGCCATTAGAGGCCACCACACCAGACG 27 > ||||||||||||||||||||||| =20 > Sbjct: 214 GGCCATTAGAGGCCACCACACCAG--- 238 >=20 > Die Fragmentinformationen: > FRAGMENT 0: read begin: 26 geno begin: 237 length: 1 > FRAGMENT 1: read begin: 0 geno begin: 214 length: 23 obiges Alignment zwar ein Alignment vom gleichen Score, der traceback ging = aber so: > Query: 0 AGCCATTAGAGGCCACCACACCAGACG 27 > |||||||||||||||||||||| | > Sbjct: 214 GGCCATTAGAGGCCACCACACCA---G 238 Bei mehreren gleich guten Alignments wird zufaellig ein traceback genommen. Mit AlignConfig sollte dein oberes Alignment raus= kommen. Gr=FC=DFe, Tobias > -----Urspr=FCngliche Nachricht----- > Von: seqan-dev-bounces@lists.fu-berlin.de=20 > [mailto:seqan-dev-bounces@lists.fu-berlin.de] Im Auftrag von=20 > Hannes Hauswedell > Gesendet: Tuesday, August 18, 2009 5:06 PM > An: Rausch, Tobias > Cc: 'seqan-dev@lists.fu-berlin.de'; 'David Weese' > Betreff: Re: [Seqan-dev] Lokales Banded-Alignment >=20 > Hallo Tobias, >=20 > danke f=FCr die schnelle Antwort! >=20 > Am Dienstag, 18. August 2009 09:46:41 schrieb Rausch, Tobias: > > Hallo Hannes, > > > > > K=E4me ich im Nachhinein noch an den Score an der Stelle x,y in der=20 > > > DP-Matrix dran? > > > > Leider nein, Gotoh, BandedGotoh & Co. speichern alle immer nur eine=20 > > Spalte bei der Berechnung um Memory zu sparen. >=20 > Hm, macht Sinn. >=20 > > > localAlignment() kann ich daf=FCr nicht verwenden, weil das=20 > kein Gotoh=20 > > > und erst Recht kein BandedGotoh unterst=FCtzt. > > > > Der SmithWaterman hinter dem localAlignment() verwendet lineare=20 > > Gapkosten ist also ein "Gotoh-Style" Algorithmus. >=20 > Da kann ich auch andere gapOpen, als gapExtend-Kosten angeben? >=20 > > Was in der Tat noch > > fehlt in SeqAn ist ein BandedSmithWaterman. > > > > > Das Problem hierbei ist, das auch mit dieser AlignConfig, das Max=20 > > > nur in letzter Zeile und Spalte, nicht aber "mittendrin" > > > gesucht wird (die Funktion ist schlie=DFlich "globalAlignment"). > > > > Ja stimmt, was du vermutlich brauchst ist der=20 > BandedSmithWaterman und=20 > > den gibt es leider noch nicht, sorry. >=20 > Obwohl ein lokales Banded ja auch nicht so sinnvoll ist, wie=20 > ein (semi-)globales Banded, da bei einem wirklich lokalen=20 > Alignment die Wahrscheinlichtkeit ja auch nicht h=F6her ist im=20 > Band / in Entfernung k um die Hauptdiagonale zu sein, als=20 > irgendwo anders. Insofern ist das Problem vielleicht viel=20 > tiefer und die Frage ob wir wirklich on lokales Alignment=20 > wollen, und wenn ja, dass wir es dann anders realisieren m=FCssen. > Aber da kann mir nur David weiterhelfen, denke ich. >=20 > Bez=FCglich dem globalAlignment und der R=FCckgabe von Fragmenten=20 > habe ich aber noch einige Verst=E4ndnissprobleme. David meinte=20 > die Fragmente seien die exakten St=FCcke des Alignments, so=20 > dass ich vor dem ersten Fragment und nach dem letzten=20 > "abschneiden" kann um "lokaler" zu werden. In der Realit=E4t=20 > bekomme ich aber ganz andere "unlokale" Ergebnisse, z.B: >=20 > Query: 0 AGCCATTAGAGGCCACCACACCAGACG 27 > ||||||||||||||||||||||| =20 > Sbjct: 214 GGCCATTAGAGGCCACCACACCAG--- 238 >=20 > Die Fragmentinformationen: > FRAGMENT 0: read begin: 26 geno begin: 237 length: 1 > FRAGMENT 1: read begin: 0 geno begin: 214 length: 23 >=20 > Woher kommt da das 0te Fragment, und wieso beginnt das erste=20 > mit einem Mismatch? (Hier ist der Read vollst=E4ndig also=20 > semiglobal aliniert) >=20 > Ein anderer Hit ist wiederum tats=E4chlicher lokaler, endet=20 > jedoch auch mit einem MisMatch: >=20 > Query: 6 CCATTAGAGGCCACCACACCG 27 > |||||||||||||||||||| > Sbjct: 216 CCATTAGAGGCCACCACACCA 237 >=20 > Unabh=E4ngig von den Fragmenten, bezieht sich der Score auch=20 > auf das echte globale Alignment, weicht also von dem hier=20 > gezeigten stark ab. >=20 > Das w=E4re ein weiterer Grund warum das Verfahren ungeeignet=20 > ist, wobei ich nat=FCrlich Alignments die den Read nicht=20 > vollst=E4ndig enthalten ein zweites Mal scoren k=F6nnte (was im=20 > Endeffekt - wie erw=E4hnt - dann aber wahrscheinlich den=20 > Geschwindigkeitsvorteil vom Banded kaputt macht). >=20 > Danke f=FCr die Hilfe, > Gru=DF, > Hannes >=20 > > > > > -----Urspr=FCngliche Nachricht----- > > > Von: seqan-dev-bounces@lists.fu-berlin.de > > > [mailto:seqan-dev-bounces@lists.fu-berlin.de] Im Auftrag=20 > von Hannes=20 > > > Hauswedell > > > Gesendet: Tuesday, August 18, 2009 1:09 AM > > > An: David Weese > > > Cc: seqan-dev@lists.fu-berlin.de > > > Betreff: [Seqan-dev] Lokales Banded-Alignment > > > > > > Hallo David und andere, > > > > > > ich versuche bei mir ein lokales Banded-Alignment mit Gotoh zu=20 > > > machen. > > > Daf=FCr benutzte ich bis jetzt: > > > > > > TScoreValue myScore =3D globalAlignment(result_frags, pairSet, > > > options.blastScoring, > > > > > > AlignConfig(), > > > diagLow, diagHigh, > > > BandedGotoh() ); > > > > > > Das Problem hierbei ist, das auch mit dieser AlignConfig, das Max=20 > > > nur in letzter Zeile und Spalte, nicht aber "mittendrin" > > > gesucht wird (die Funktion ist schlie=DFlich "globalAlignment"). > > > Ich k=F6nnte nat=FCrlich von Beginn des ersten Fragments bis zum Ende= =20 > > > des letzten nochmal global scoren, aber das ist ein extra Aufruf,=20 > > > der das Gesamte noch weiter bremst (dieser=20 > Funktionsaufruf ist jetzt=20 > > > schon der Bottleneck). > > > > > > localAlignment() kann ich daf=FCr nicht verwenden, weil das=20 > kein Gotoh=20 > > > und erst Recht kein BandedGotoh unterst=FCtzt. > > > > > > Was kann man da tun? K=E4me ich im Nachhinein noch an den=20 > Score an der=20 > > > Stelle x,y in der DP-Matrix dran? x,y w=E4re hierbei das Ende des=20 > > > letzten Fragments (bzw. wegen reverser Orientierung, des ersten). > > > > > > Vielen Dank, > > > Hannes > > > > > > _______________________________________________ > > > seqan-dev mailing list > > > seqan-dev@lists.fu-berlin.de > > > https://lists.fu-berlin.de/listinfo/seqan-dev >=20 > -- > Solidarische Gr=FC=DFe > Hannes >=20 > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev > = From rsteinfelder@uni-bielefeld.de Thu Aug 20 15:58:54 2009 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1Me8AH-0005a9-VH>; Thu, 20 Aug 2009 15:58:54 +0200 Received: from mux1-unibi-smtp.hrz.uni-bielefeld.de ([129.70.204.65]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1Me8AH-0002qe-TS>; Thu, 20 Aug 2009 15:58:53 +0200 MIME-version: 1.0 Content-disposition: inline Content-type: text/plain; charset=iso-8859-1 Received: from pmxchannel-daemon.mux1-unibi-smtp.hrz.uni-bielefeld.de by mux1-unibi-smtp.hrz.uni-bielefeld.de (Sun Java(tm) System Messaging Server 6.3-6.03 (built Mar 14 2008; 32bit)) id <0KOO00C00HI5Q700@mux1-unibi-smtp.hrz.uni-bielefeld.de> for seqan-dev@lists.fu-berlin.de; Thu, 20 Aug 2009 15:58:53 +0200 (CEST) Received: from udp9945496uds.dhcp.uni-bielefeld.de ([129.70.166.236]) by mux1-unibi-smtp.hrz.uni-bielefeld.de (Sun Java(tm) System Messaging Server 6.3-6.03 (built Mar 14 2008; 32bit)) with ESMTPPSA id <0KOO00CJGHI5GL00@mux1-unibi-smtp.hrz.uni-bielefeld.de> for seqan-dev@lists.fu-berlin.de; Thu, 20 Aug 2009 15:58:53 +0200 (CEST) Date: Thu, 20 Aug 2009 15:57:41 +0200 From: Robert Steinfelder To: seqan-dev@lists.fu-berlin.de Message-id: <1148_1250776733_ZZg0C3P0kWBjv.00_200908201557.42021.rsteinfelder@uni-bielefeld.de> Organization: University of Bielefeld Content-transfer-encoding: quoted-printable X-EnvFrom: rsteinfelder@uni-bielefeld.de X-PMX-Version: 5.5.1.360522, Antispam-Engine: 2.6.1.350677, Antispam-Data: 2009.8.20.135117, pmx7 X-Connecting-IP: 129.70.166.236 User-Agent: KMail/1.9.10 X-Originating-IP: 129.70.204.65 X-purgate: clean X-purgate-ID: 151147::1250776733-000059FE-3B03AD87/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.002285, version=1.1.6 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Benin.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=-0.0 required=5.0 tests=SPF_HELO_PASS,SPF_PASS Subject: [Seqan-dev] Allgemeine Scores verwenden? X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 Precedence: list List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Thu, 20 Aug 2009 13:58:54 -0000 Hallo, ich habe einen Algorithmus in SeqAn implementiert. Dieser soll anhand einer= =20 ScoreMatrix, einem Alignment und einer Sequenz einen =C4hnlichkeitsscore=20 zur=FCckliefern. Derzeit funktioniert dieser aber nur mit einfachen Scores= =20 (Mis-/Match, GapOpen, GapExtension), aber nicht mit z.B. einer Blosum62. Wie kann man allgemein mit komplexeren Scores arbeiten? Gru=DF,=20 Robert Steinfelder From Tobias.Rausch@fu-berlin.de Thu Aug 20 16:29:21 2009 Received: from outpost1.zedat.fu-berlin.de ([130.133.4.66]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1Me8dj-0006Se-5g>; Thu, 20 Aug 2009 16:29:19 +0200 Received: from relay2.zedat.fu-berlin.de ([130.133.4.80]) by outpost1.zedat.fu-berlin.de (Exim 4.69) with esmtp (envelope-from ) id <1Me8dj-0002Xg-4H>; Thu, 20 Aug 2009 16:29:19 +0200 Received: from exchange6.fu-berlin.de ([160.45.9.133]) by relay2.zedat.fu-berlin.de (Exim 4.69) with esmtp (envelope-from ) id <1Me8dj-0005oL-0s>; Thu, 20 Aug 2009 16:29:19 +0200 Received: from exchange6.fu-berlin.de ([160.45.9.133]) by exchange6.fu-berlin.de ([160.45.9.133]) with mapi; Thu, 20 Aug 2009 16:29:19 +0200 From: "Rausch, Tobias" To: 'Robert Steinfelder' , "'seqan-dev@lists.fu-berlin.de'" Date: Thu, 20 Aug 2009 16:29:18 +0200 Thread-Topic: [Seqan-dev] Allgemeine Scores verwenden? Thread-Index: Acohnlyi521G4J68Q+uP61SJ0iPNQQAAmytA Message-ID: <6AB91D0276C1E744892C72E49C9DFFF7376A48997A@exchange6.fu-berlin.de> References: <1148_1250776733_ZZg0C3P0kWBjv.00_200908201557.42021.rsteinfelder@uni-bielefeld.de> In-Reply-To: <1148_1250776733_ZZg0C3P0kWBjv.00_200908201557.42021.rsteinfelder@uni-bielefeld.de> Accept-Language: en-US, de-DE Content-Language: de-DE X-MS-Has-Attach: X-MS-TNEF-Correlator: acceptlanguage: en-US, de-DE Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 X-Originating-IP: 160.45.9.133 X-purgate: clean X-purgate-ID: 151147::1250778559-000059FE-3DCCAFF7/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.009752, version=1.1.6 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Togo.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED Subject: Re: [Seqan-dev] Allgemeine Scores verwenden? X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 Precedence: list List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Thu, 20 Aug 2009 14:29:21 -0000 Hallo Robert, In ./seqan/score/score_base.h ist das Interface der Score-Objekte definiert= . score(TScore&, TPos1, TPos2, TSeq1&, TSeq2&) scoreGapOpenHorizontal(TScore&, TPos1, TPos2, TSeq1&, TSeq2&) scoreGapExtendHorizontal(TScore&, TPos1, TPos2, TSeq1&, TSeq2&) scoreGapOpenVertical(TScore&, TPos1, TPos2, TSeq1&, TSeq2&) scoreGapExtendVertical(TScore&, TPos1, TPos2, TSeq1&, TSeq2&) Das Interface erlaubt ein position-dependent scoring, deshalb werden immer die beiden Sequenzen und die 2 Positionen uebergeben und Scoreobjekt.= Das funktioniert auf Score, Blosum62, etc. Vielleicht kannst du das Interface auch verwenden. Gr=FC=DFe, Tobias > -----Urspr=FCngliche Nachricht----- > Von: seqan-dev-bounces@lists.fu-berlin.de=20 > [mailto:seqan-dev-bounces@lists.fu-berlin.de] Im Auftrag von=20 > Robert Steinfelder > Gesendet: Thursday, August 20, 2009 3:58 PM > An: seqan-dev@lists.fu-berlin.de > Betreff: [Seqan-dev] Allgemeine Scores verwenden? >=20 > Hallo, >=20 > ich habe einen Algorithmus in SeqAn implementiert. Dieser=20 > soll anhand einer ScoreMatrix, einem Alignment und einer=20 > Sequenz einen =C4hnlichkeitsscore zur=FCckliefern. Derzeit=20 > funktioniert dieser aber nur mit einfachen Scores=20 > (Mis-/Match, GapOpen, GapExtension), aber nicht mit z.B.=20 > einer Blosum62. >=20 > Wie kann man allgemein mit komplexeren Scores arbeiten? >=20 >=20 > Gru=DF, > Robert Steinfelder >=20 > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev > = From andres.burgos@irisa.fr Fri Aug 21 18:01:47 2009 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1MeWYj-0008Qz-8M>; Fri, 21 Aug 2009 18:01:46 +0200 Received: from mail1-relais-roc.national.inria.fr ([192.134.164.82]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1MeWYj-0005wV-5l>; Fri, 21 Aug 2009 18:01:45 +0200 From: andres.burgos@irisa.fr X-IronPort-AV: E=Sophos;i="4.44,251,1249250400"; d="scan'208";a="34679124" Received: from omel.irisa.fr (HELO mail.irisa.fr) ([131.254.254.102]) by mail1-relais-roc.national.inria.fr with ESMTP; 21 Aug 2009 18:01:44 +0200 Received: from 131.254.10.65 (SquirrelMail authenticated user aburgos) by mail.irisa.fr with HTTP; Fri, 21 Aug 2009 18:01:44 +0200 Message-ID: <4cdd147ccc281be49aabfc1f18b1245b.squirrel@mail.irisa.fr> Date: Fri, 21 Aug 2009 18:01:44 +0200 To: seqan-dev@lists.fu-berlin.de User-Agent: SquirrelMail/1.4.19 MIME-Version: 1.0 Content-Type: text/plain;charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Priority: 3 (Normal) Importance: Normal X-Originating-IP: 192.134.164.82 X-purgate: clean X-purgate-ID: 151147::1250870505-000059FE-C1D2EC93/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000202, version=1.1.6 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Niger.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=0.2 required=5.0 tests=NO_REAL_NAME Subject: [Seqan-dev] multiLocalAlignment function X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 Precedence: list List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Fri, 21 Aug 2009 16:01:47 -0000 Hi! I'm currently trying to make work the function multiLocalAlignment(graph, edgeMap, score, numAlign, tag) but I can't success, so I was hoping to get some help, since it's not documented on the web site. I was also wondering weather this function would return overlapping or non-overlapping alignments. Ok, so here is the code I'm working on: typedef seqan::String TString; typedef seqan::StringSet > TStringSet; typedef seqan::Graph > TGraph; TStringSet str; TString s1 ("some string"); TString s2 ("some other string"); seqan::appendValue(str, s1); seqan::appendValue(str, s2); seqan::Score > pam (250, -1, 0); TGraph g(str); seqan::String > > propMap; seqan::resizeEdgeMap(g, propMap); seqan::multiLocalAlignment(g, propMap, pam, 10, seqan::SmithWaterman()); This won't compile, throwing this error: ../seqan-1.1/seqan/graph_align/graph_align_interface.h: In function �void seqan::multiLocalAlignment(seqan::Graph >&, TPropertyMap&, const seqan::Score&, TSize, TTag) [with TStringSet = seqan::StringSet, seqan::Alloc >, seqan::Dependent > >, TCargo = seqan::SimpleType, TSpec = const seqan::Tag, TPropertyMap = seqan::String, seqan::StorePointsOnly>, seqan::Alloc >, TScoreValue = int, TSpec2 = seqan::Pam, seqan::Pam_Data_Dayhoff_MDM78>, TSize = int, TTag = seqan::Tag]�: readers/SWReader.cc:26: instantiated from here ../seqan-1.1/seqan/graph_align/graph_align_interface.h:234: error: no matching function for call to �_localAlignment(seqan::String > >, seqan::Alloc >&, seqan::StringSet, seqan::Alloc >, seqan::Dependent > >&, seqan::String, seqan::StorePointsOnly>, seqan::Alloc >&, const seqan::Score, seqan::Pam_Data_Dayhoff_MDM78> >&, int&, seqan::Tag)� make: *** [readers/SWReader.o] Error 1 So, maybe an example would make things clearer... Thanks in advance, Andres From Tobias.Rausch@fu-berlin.de Sun Aug 23 16:37:11 2009 Received: from outpost2.zedat.fu-berlin.de ([130.133.4.90]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1MfEBx-0002qG-5N>; Sun, 23 Aug 2009 16:37:09 +0200 Received: from relay2.zedat.fu-berlin.de ([130.133.4.80]) by outpost1.zedat.fu-berlin.de (Exim 4.69) with esmtp (envelope-from ) id <1MfEBx-0007NZ-2E>; Sun, 23 Aug 2009 16:37:09 +0200 Received: from exchange6.fu-berlin.de ([160.45.9.133]) by relay2.zedat.fu-berlin.de (Exim 4.69) with esmtp (envelope-from ) id <1MfEBw-0002JQ-Ub>; Sun, 23 Aug 2009 16:37:09 +0200 Received: from exchange6.fu-berlin.de ([160.45.9.133]) by exchange6.fu-berlin.de ([160.45.9.133]) with mapi; Sun, 23 Aug 2009 16:37:09 +0200 From: "Rausch, Tobias" To: "andres.burgos@irisa.fr" , "seqan-dev@lists.fu-berlin.de" Date: Sun, 23 Aug 2009 16:37:08 +0200 Thread-Topic: [Seqan-dev] multiLocalAlignment function Thread-Index: AcoieLJr8OBRLVSBShSd0ICt/ciUFABhWCqA Message-ID: <6AB91D0276C1E744892C72E49C9DFFF7376A5B2843@exchange6.fu-berlin.de> References: <4cdd147ccc281be49aabfc1f18b1245b.squirrel@mail.irisa.fr> In-Reply-To: <4cdd147ccc281be49aabfc1f18b1245b.squirrel@mail.irisa.fr> Accept-Language: en-US, de-DE Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: acceptlanguage: en-US, de-DE Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 X-Originating-IP: 160.45.9.133 X-purgate: clean X-purgate-ID: 151147::1251038229-000059FE-4AF9BD92/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.136801, version=1.1.6 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Kenia.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED Subject: Re: [Seqan-dev] multiLocalAlignment function X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 Precedence: list List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Sun, 23 Aug 2009 14:37:11 -0000 Hello Andres, The multi-local alignment algorithm we have implemented is the one from Wat= erman and Eggert. It returns possibly overlapping local alignments, so it is not a repeated m= atch finder. It is implemented in ./seqan/graph_align/graph_align_smith_waterman_clump.h= and as you can see at the bottom of the file it repeatedly calls the standard s= mith-waterman alignment algorithm. Each found local alignment is then forbidden in the ne= xt run. I send you an example on how to use it on Monday. Best regards, Tobias ________________________________________ From: seqan-dev-bounces@lists.fu-berlin.de [seqan-dev-bounces@lists.fu-berl= in.de] On Behalf Of andres.burgos@irisa.fr [andres.burgos@irisa.fr] Sent: Friday, August 21, 2009 6:01 PM To: seqan-dev@lists.fu-berlin.de Subject: [Seqan-dev] multiLocalAlignment function Hi! I'm currently trying to make work the function multiLocalAlignment(graph, edgeMap, score, numAlign, tag) but I can't success, so I was hoping to get some help, since it's not documented on the web site. I was also wondering weather this function would return overlapping or non-overlapping alignments. Ok, so here is the code I'm working on: typedef seqan::String TString; typedef seqan::StringSet > TStringSet; typedef seqan::Graph > TGraph; TStringSet str; TString s1 ("some string"); TString s2 ("some other string"); seqan::appendValue(str, s1); seqan::appendValue(str, s2); seqan::Score > pam (250, -1, 0); TGraph g(str); seqan::String > > propMap; seqan::resizeEdgeMap(g, propMap); seqan::multiLocalAlignment(g, propMap, pam, 10, seqan::SmithWaterman())= ; This won't compile, throwing this error: ../seqan-1.1/seqan/graph_align/graph_align_interface.h: In function =91void seqan::multiLocalAlignment(seqan::Graph >&, TPropertyMap&, const seqan::Score&, TSize, TTag) [with TStringSet =3D seqan::StringSet, seqan::Alloc >, seqan::Dependent > >, TCargo =3D seqan::SimpleType, TSpec =3D const seqan::Tag, TPropertyMap =3D seqan::String, seqan::StorePointsOnly>, seqan::Alloc >, TScoreValue =3D int, TSpec2 = =3D seqan::Pam, seqan::Pam_Data_Dayhoff_MDM78>, TSize =3D int, TTag =3D seqan::Tag]=92: readers/SWReader.cc:26: instantiated from here ../seqan-1.1/seqan/graph_align/graph_align_interface.h:234: error: no matching function for call to =91_localAlignment(seqan::String > >, seqan::Alloc >&, seqan::StringSet, seqan::Alloc >, seqan::Dependent > >&, seqan::String, seqan::StorePointsOnly>, seqan::Alloc >&, const seqan::Score, seqan::Pam_Data_Dayhoff_MDM78> >&, int&, seqan::Tag)=92 make: *** [readers/SWReader.o] Error 1 So, maybe an example would make things clearer... Thanks in advance, Andres _______________________________________________ seqan-dev mailing list seqan-dev@lists.fu-berlin.de https://lists.fu-berlin.de/listinfo/seqan-dev From hauswedell@mi.fu-berlin.de Sun Aug 23 18:37:32 2009 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1MfG4R-0006C1-LD>; Sun, 23 Aug 2009 18:37:31 +0200 Received: from einhorn.in-berlin.de ([192.109.42.8]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1MfG4R-0007gh-Ic>; Sun, 23 Aug 2009 18:37:31 +0200 X-Envelope-From: hauswedell@mi.fu-berlin.de X-Envelope-To: Received: from fbsdlap.freedom.lan (soulrebel.in-vpn.de [217.197.85.84]) (authenticated bits=0) by einhorn.in-berlin.de (8.13.6/8.13.6/Debian-1) with ESMTP id n7NGbTb2005417 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT) for ; Sun, 23 Aug 2009 18:37:30 +0200 From: Hannes Hauswedell To: seqan-dev@lists.fu-berlin.de Date: Sun, 23 Aug 2009 18:37:27 +0200 User-Agent: KMail/1.12.0 (FreeBSD/7.2-PRERELEASE; KDE/4.3.0; i386; ; ) MIME-Version: 1.0 Content-Type: Multipart/Mixed; boundary="Boundary-00=_HBXkKQ9T8nsG7cP" Message-Id: <200908231837.27473.hauswedell@mi.fu-berlin.de> X-Scanned-By: MIMEDefang_at_IN-Berlin_e.V. on 192.109.42.8 X-Originating-IP: 192.109.42.8 X-ZEDAT-Hint: A X-purgate: clean X-purgate-ID: 151147::1251045451-000059FE-89E16EC3/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.1.6 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Kenia.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=0.1 required=5.0 tests=FORGED_RCVD_HELO Subject: [Seqan-dev] Scoring mit Blosum62 X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 Precedence: list List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Sun, 23 Aug 2009 16:37:32 -0000 --Boundary-00=_HBXkKQ9T8nsG7cP Content-Type: Text/Plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hallo wieder! bez. der lokal/semi-global-Frage warte ich auf Antwort von David. Ich bin gerade an dem BLASTX-Modus meiner Bachelor-Arbeit. Dabei komme=20 ich nicht weiter. Ich m=F6chte einfach mit einer Blosum62 ein Alignment=20 scoren, dazu benutze ich als Aufruf (jenach Option wird hier das=20 Nucleotide oder das Protein-Scoring verwendet): int score =3D globalAlignment(align, (options.blastMode =3D=3D 1) ? options.blastNScoring : options.blastPScoring, Gotoh()); Vorher habe ich das nur mit blastNScoring gemacht, problemlos.=20 BlastNScoring ist vom Typ Score, BlastPScoring ist vom Typ=20 Blosum62.=20 Der Compiler spuckt dabei als Fehler aus: /usr/include/c++/4.2/bits/stl_algobase.h:283: error: cannot convert=20 'seqan::Score' to 'char' in assignment Die etwas l=E4ngeren Vorlauf habe ich angehangen. Danke f=FCr Tipps! Gru=DF, Hannes --Boundary-00=_HBXkKQ9T8nsG7cP Content-Type: text/x-log; charset="UTF-8"; name="blosum62_build_error.log" Content-Transfer-Encoding: quoted-printable Content-Disposition: attachment; filename="blosum62_build_error.log" /usr/include/c++/4.2/bits/stl_algobase.h: In static member function 'static= _OI std::__copy<_BoolType, std::random_access_iterator_tag>::copy(_II, _II= , _OI) [with _II =3D seqan::Score*, _OI =3D char*, bool= _BoolType =3D false]': = =20 /usr/include/c++/4.2/bits/stl_algobase.h:315: instantiated from '_OI std:= :__copy_aux(_II, _II, _OI) [with _II =3D seqan::Score*,= _OI =3D char*]' = = =20 /usr/include/c++/4.2/bits/stl_algobase.h:340: instantiated from 'static _= OI std::__copy_normal<, >::__copy_n(_II, _II, _OI) [= with _II =3D seqan::Score*, _OI =3D char*, bool =3D false, bool =3D false]' = =20 /usr/include/c++/4.2/bits/stl_algobase.h:401: instantiated from '_OutputI= terator std::copy(_InputIterator, _InputIterator, _OutputIterator) [with _I= nputIterator =3D seqan::Score*, _OutputIterator =3D cha= r*]' = =20 /home/hannes/devel/seqan/teaching/master/hauswedell/razerblasts/../../../..= /seqan/projects/library/seqan/basic/basic_alphabet_interface.h:509: insta= ntiated from 'void seqan::_arrayCopyForward_Default(TSource1, TSource2, TTa= rget) [with TTarget =3D char*, TSource1 =3D seqan::Score*, TSource2 =3D seqan::Score*]' = = = = =20 /home/hannes/devel/seqan/teaching/master/hauswedell/razerblasts/../../../..= /seqan/projects/library/seqan/basic/basic_alphabet_interface.h:518: insta= ntiated from 'void seqan::arrayCopyForward(TSource1, TSource2, TTarget) [wi= th TTarget =3D char*, TSource1 =3D seqan::Score*, TSour= ce2 =3D seqan::Score*]' = = = = =20 /home/hannes/devel/seqan/teaching/master/hauswedell/razerblasts/../../../..= /seqan/projects/library/seqan/basic/basic_alphabet_trait_basic.h:102: ins= tantiated from 'void seqan::_arrayConstructCopy_Pointer(TValueSource*, TVal= ueSource*, TValueTarget*, seqan::True) [with TValueSource =3D seqan::Score<= int, seqan::Simple>, TValueTarget =3D char]' = = = = =20 /home/hannes/devel/seqan/teaching/master/hauswedell/razerblasts/../../../..= /seqan/projects/library/seqan/basic/basic_alphabet_trait_basic.h:132: ins= tantiated from 'void seqan::arrayConstructCopy(TValueSource*, TValueSource*= , TValueTarget*) [with TValueSource =3D seqan::Score, T= ValueTarget =3D char]' =20 /home/hannes/devel/seqan/teaching/master/hauswedell/razerblasts/../../../..= /seqan/projects/library/seqan/sequence/string_base.h:764: instantiated fr= om 'static void seqan::_Assign_String::assign_(TTarget&, TSource&)= [with TTarget =3D seqan::String >, TSource =3D co= nst seqan::String, seqan::Alloc >, T= Expand =3D const seqan::Tag]' = = = =20 /home/hannes/devel/seqan/teaching/master/hauswedell/razerblasts/../../../..= /seqan/projects/library/seqan/sequence/string_base.h:812: instantiated fr= om 'void seqan::assign(seqan::String&, const TSource&, seqan= ::Tag) [with TTargetValue =3D char, TTargetSpec =3D seqan::Alloc, TSource =3D seqan::String, seqan::All= oc >, TExpand =3D seqan::TagGenerous_]' = = = =20 /home/hannes/devel/seqan/teaching/master/hauswedell/razerblasts/../../../..= /seqan/projects/library/seqan/sequence/string_base.h:772: instantiated fr= om 'static void seqan::_Assign_String::assign_(TTarget&, TSource&)= [with TTarget =3D seqan::String >, TSource =3D co= nst seqan::Score, TExpand =3D const seqan::Tag]' = = = =20 /home/hannes/devel/seqan/teaching/master/hauswedell/razerblasts/../../../..= /seqan/projects/library/seqan/sequence/string_base.h:812: instantiated fr= om 'void seqan::assign(seqan::String&, const TSource&, seqan= ::Tag) [with TTargetValue =3D char, TTargetSpec =3D seqan::Alloc, TSource =3D seqan::Score, TExpand =3D seqan::TagGe= nerous_]' = = = =20 /home/hannes/devel/seqan/teaching/master/hauswedell/razerblasts/../../../..= /seqan/projects/library/seqan/sequence/string_base.h:746: instantiated fr= om 'void seqan::assign(seqan::String&, const TSource&) [with= TTargetValue =3D char, TTargetSpec =3D seqan::Alloc, TSource =3D seq= an::Score]' =20 /home/hannes/devel/seqan/teaching/master/hauswedell/razerblasts/../../../..= /seqan/projects/library/seqan/sequence/string_alloc.h:79: instantiated fr= om 'seqan::String >::String(const TSource&) [wit= h TSource =3D seqan::Score, TValue =3D char]' = =20 /home/hannes/devel/seqan/teaching/master/hauswedell/razerblasts/../../../..= /seqan/projects/library/seqan/score/score_matrix.h:312: instantiated from= 'void seqan::loadScoreMatrix(seqan::Score >&, TString&) [with TValue =3D int, TSequenceValue =3D se= qan::SimpleType, TSpec =3D seqan::_Blosum= 62, TString =3D const seqan::Score]' = = = =20 /home/hannes/devel/seqan/teaching/master/hauswedell/razerblasts/../../../..= /seqan/projects/library/seqan/score/score_matrix.h:92: instantiated from = 'seqan::Score >::Score(co= nst TString&, TValue) [with TString =3D seqan::Score, T= Value =3D int, TSequenceValue =3D seqan::SimpleType, TSpec =3D seqan::_Blosum62]' = = = =20 /home/hannes/devel/seqan/teaching/master/hauswedell/razerblasts/outputForma= t_withBlast.h:1132: instantiated from 'void seqan::dumpMatches(TMatches&,= const TGenomeNames&, seqan::StringSet >, seqan::Owner > >&, std::map, std::alloc= ator >, unsigned int>, std::less, std::allocator, std::allocator >, unsigned int> > > >&, const TReads&, TCounts= &, const TReadNames&, std::string, std::string, seqan::RazerSOptions= &) [with TMatches =3D seqan::String, seqan::Alloc >, TGenomeNames =3D seqan::StringSet >, seqan::Owner > >, TReads =3D seqan= ::StringSet, = seqan::Alloc >, seqan::Owner > >, TReadName= s =3D seqan::StringSet >, seqan::Own= er > >, TCounts =3D seqan::String >, seqan::Alloc >, TSpe= c =3D seqan::RazerBlastSSpec]' /home/hannes/devel/seqan/teaching/master/hauswedell/razerblasts/razer_blast= _s.cpp:191: instantiated from 'int mapReads(const char*, const char**, co= nst char*, seqan::RazerSOptions&) [with TSpec =3D seqan::RazerBlastS= Spec]' /home/hannes/devel/seqan/teaching/master/hauswedell/razerblasts/razer_blast= _s.cpp:1636: instantiated from here /usr/include/c++/4.2/bits/stl_algobase.h:283: error: cannot convert 'seqan:= :Score' to 'char' in assignment gmake[2]: *** [CMakeFiles/razerblasts.dir/razer_blast_s.cpp.o] Fehler 1 gmake[1]: *** [CMakeFiles/razerblasts.dir/all] Fehler 2 gmake: *** [all] Fehler 2 --Boundary-00=_HBXkKQ9T8nsG7cP-- From andres.burgos@irisa.fr Sun Aug 23 19:54:33 2009 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1MfHGx-0008L5-Co>; Sun, 23 Aug 2009 19:54:31 +0200 Received: from mail2-relais-roc.national.inria.fr ([192.134.164.83]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1MfHGx-0003EY-9Y>; Sun, 23 Aug 2009 19:54:31 +0200 From: andres.burgos@irisa.fr X-IronPort-AV: E=Sophos;i="4.44,260,1249250400"; d="scan'208";a="31509170" Received: from omel.irisa.fr (HELO mail.irisa.fr) ([131.254.254.102]) by mail2-relais-roc.national.inria.fr with ESMTP; 23 Aug 2009 19:54:30 +0200 Received: from 193.52.94.5 (SquirrelMail authenticated user aburgos) by mail.irisa.fr with HTTP; Sun, 23 Aug 2009 19:54:30 +0200 Message-ID: <70eafd2b63c4ffbd2457da559310d1bb.squirrel@mail.irisa.fr> In-Reply-To: <6AB91D0276C1E744892C72E49C9DFFF7376A5B2843@exchange6.fu-berlin.de> References: <4cdd147ccc281be49aabfc1f18b1245b.squirrel@mail.irisa.fr> <6AB91D0276C1E744892C72E49C9DFFF7376A5B2843@exchange6.fu-berlin.de> Date: Sun, 23 Aug 2009 19:54:30 +0200 To: "Rausch, Tobias" User-Agent: SquirrelMail/1.4.19 MIME-Version: 1.0 Content-Type: text/plain;charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Priority: 3 (Normal) Importance: Normal X-Originating-IP: 192.134.164.83 X-purgate: clean X-purgate-ID: 151147::1251050071-000059FE-03612D97/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.1.6 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Niger.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=0.2 required=5.0 tests=NO_REAL_NAME Cc: "seqan-dev@lists.fu-berlin.de" Subject: Re: [Seqan-dev] multiLocalAlignment function X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 Precedence: list List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Sun, 23 Aug 2009 17:54:33 -0000 Hi Tobias, thanks for your reply, I'll take a closer look at the code so maybe I'll figure it out, but the example will still be helpful. Danke schoen! Andres > Hello Andres, > > The multi-local alignment algorithm we have implemented is the one from > Waterman and Eggert. > It returns possibly overlapping local alignments, so it is not a repeated > match finder. > > It is implemented in > ./seqan/graph_align/graph_align_smith_waterman_clump.h and > as you can see at the bottom of the file it repeatedly calls the standard > smith-waterman > alignment algorithm. Each found local alignment is then forbidden in the > next run. > > I send you an example on how to use it on Monday. > > Best regards, > Tobias > > > ________________________________________ > From: seqan-dev-bounces@lists.fu-berlin.de > [seqan-dev-bounces@lists.fu-berlin.de] On Behalf Of andres.burgos@irisa.fr > [andres.burgos@irisa.fr] > Sent: Friday, August 21, 2009 6:01 PM > To: seqan-dev@lists.fu-berlin.de > Subject: [Seqan-dev] multiLocalAlignment function > > Hi! > > I'm currently trying to make work the function > > multiLocalAlignment(graph, edgeMap, score, numAlign, tag) > > but I can't success, so I was hoping to get some help, since it's not > documented on the web site. I was also wondering weather this function > would return overlapping or non-overlapping alignments. > > Ok, so here is the code I'm working on: > > typedef seqan::String TString; > typedef seqan::StringSet > TStringSet; > typedef seqan::Graph > > TGraph; > > TStringSet str; > TString s1 ("some string"); > TString s2 ("some other string"); > > seqan::appendValue(str, s1); > seqan::appendValue(str, s2); > > seqan::Score > pam (250, -1, 0); > TGraph g(str); > > seqan::String int> > > propMap; > seqan::resizeEdgeMap(g, propMap); > > seqan::multiLocalAlignment(g, propMap, pam, 10, > seqan::SmithWaterman()); > > This won't compile, throwing this error: > > ../seqan-1.1/seqan/graph_align/graph_align_interface.h: In function �void > seqan::multiLocalAlignment(seqan::Graph TCargo, TSpec> >&, TPropertyMap&, const seqan::Score TSpec2>&, TSize, TTag) [with TStringSet = > seqan::StringSet seqan::_AminoAcid>, seqan::Alloc >, seqan::Dependent seqan::Tag > >, TCargo = seqan::SimpleType char, seqan::_AminoAcid>, TSpec = const seqan::Tag, > TPropertyMap = > seqan::String, > seqan::StorePointsOnly>, seqan::Alloc >, TScoreValue = int, TSpec2 = > seqan::Pam, > seqan::Pam_Data_Dayhoff_MDM78>, TSize = int, TTag = > seqan::Tag]�: > readers/SWReader.cc:26: instantiated from here > ../seqan-1.1/seqan/graph_align/graph_align_interface.h:234: error: no > matching function for call to > �_localAlignment(seqan::String seqan::ExactFragment > >, > seqan::Alloc >&, > seqan::StringSet seqan::_AminoAcid>, seqan::Alloc >, seqan::Dependent seqan::Tag > >&, > seqan::String, > seqan::StorePointsOnly>, seqan::Alloc >&, const seqan::Score seqan::Pam, > seqan::Pam_Data_Dayhoff_MDM78> >&, int&, > seqan::Tag)� > make: *** [readers/SWReader.o] Error 1 > > So, maybe an example would make things clearer... > > Thanks in advance, > Andres > > > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev > From weese@inf.fu-berlin.de Mon Aug 24 11:13:48 2009 Received: from outpost2.zedat.fu-berlin.de ([130.133.4.90]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1MfVcZ-0001Fl-Qw>; Mon, 24 Aug 2009 11:13:47 +0200 Received: from inpost2.zedat.fu-berlin.de ([130.133.4.69]) by outpost1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1MfVcZ-0005me-PL>; Mon, 24 Aug 2009 11:13:47 +0200 Received: from [160.45.118.25] (helo=blowfish.mi.fu-berlin.de) by inpost2.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtpsa (envelope-from ) id <1MfVcZ-0003cI-MZ>; Mon, 24 Aug 2009 11:13:47 +0200 Message-ID: <4A9259CB.7030708@inf.fu-berlin.de> Date: Mon, 24 Aug 2009 11:13:47 +0200 From: David Weese User-Agent: Thunderbird 2.0.0.23 (Macintosh/20090812) MIME-Version: 1.0 To: seqan-dev@lists.fu-berlin.de References: <200908231837.27473.hauswedell@mi.fu-berlin.de> In-Reply-To: <200908231837.27473.hauswedell@mi.fu-berlin.de> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit X-Originating-IP: 160.45.118.25 X-purgate: clean X-purgate-ID: 151147::1251105227-000059FE-9016AEE4/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.1.6 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Benin.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED X-Mailman-Approved-At: Mon, 24 Aug 2009 11:15:49 +0200 Subject: Re: [Seqan-dev] Scoring mit Blosum62 X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Mon, 24 Aug 2009 09:13:48 -0000 Hallo Hannes, bin jetzt wieder zur�ck. Der Fehler unten kommt von unterschiedlichen Typen (verschiedene TSpecs) deiner Score-Objekte blastNScoring und blastPScoring, die nicht ineinander konvertiert werden k�nnen. Versuch den Einzeiler in 2 Zeilen zu schreiben, dann sollte es gehen. Gru�, David Hannes Hauswedell schrieb: > Hallo wieder! > > bez. der lokal/semi-global-Frage warte ich auf Antwort von David. > > Ich bin gerade an dem BLASTX-Modus meiner Bachelor-Arbeit. Dabei komme > ich nicht weiter. Ich m�chte einfach mit einer Blosum62 ein Alignment > scoren, dazu benutze ich als Aufruf (jenach Option wird hier das > Nucleotide oder das Protein-Scoring verwendet): > > > int score = globalAlignment(align, > (options.blastMode == 1) > ? options.blastNScoring > : options.blastPScoring, > Gotoh()); > > Vorher habe ich das nur mit blastNScoring gemacht, problemlos. > BlastNScoring ist vom Typ Score, BlastPScoring ist vom Typ > Blosum62. > > Der Compiler spuckt dabei als Fehler aus: > > /usr/include/c++/4.2/bits/stl_algobase.h:283: error: cannot convert > 'seqan::Score' to 'char' in assignment > > Die etwas l�ngeren Vorlauf habe ich angehangen. > > Danke f�r Tipps! > > Gru�, > Hannes > > ------------------------------------------------------------------------ > > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev From hauswedell@mi.fu-berlin.de Mon Aug 24 11:58:13 2009 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1MfWJZ-0002Yb-4k>; Mon, 24 Aug 2009 11:58:13 +0200 Received: from einhorn.in-berlin.de ([192.109.42.8]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1MfWJZ-0005mY-2i>; Mon, 24 Aug 2009 11:58:13 +0200 X-Envelope-From: hauswedell@mi.fu-berlin.de X-Envelope-To: Received: from fbsdlap.freedom.lan (soulrebel.in-vpn.de [217.197.85.84]) (authenticated bits=0) by einhorn.in-berlin.de (8.13.6/8.13.6/Debian-1) with ESMTP id n7O9wCKx021971 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT) for ; Mon, 24 Aug 2009 11:58:12 +0200 From: Hannes Hauswedell To: SeqAn Development Date: Mon, 24 Aug 2009 11:58:10 +0200 User-Agent: KMail/1.12.0 (FreeBSD/7.2-PRERELEASE; KDE/4.3.0; i386; ; ) References: <200908231837.27473.hauswedell@mi.fu-berlin.de> <4A9259CB.7030708@inf.fu-berlin.de> In-Reply-To: <4A9259CB.7030708@inf.fu-berlin.de> MIME-Version: 1.0 Content-Type: Text/Plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Message-Id: <200908241158.10783.hauswedell@mi.fu-berlin.de> X-Scanned-By: MIMEDefang_at_IN-Berlin_e.V. on 192.109.42.8 X-Originating-IP: 192.109.42.8 X-purgate: clean X-purgate-ID: 151147::1251107893-000059FE-0FBE09A5/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.1.6 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Gabun.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=0.1 required=5.0 tests=FORGED_RCVD_HELO Subject: Re: [Seqan-dev] Scoring mit Blosum62 X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Mon, 24 Aug 2009 09:58:14 -0000 Am Montag, 24. August 2009 11:13:47 schrieb David Weese: > Hallo Hannes, > > bin jetzt wieder zur=FCck. Der Fehler unten kommt von unterschiedlichen > Typen (verschiedene TSpecs) deiner Score-Objekte blastNScoring und > blastPScoring, die nicht ineinander konvertiert werden k=F6nnen. > Versuch den Einzeiler in 2 Zeilen zu schreiben, dann sollte es gehen. Hm, das hatte ich schon ausprobiert, weil ich dann auch dachte, dass der=20 zwei Aufrufe braucht, da die Argumente vielleicht zu zwei=20 unterschiedlichen Funktionen aufl=F6sen. Hatte das wohl aber nur an einer=20 Stelle ersetzt... jetzt gehts, danke. Hast du dir bez=FCglich der lokal-global-Frage schon Gedanken gemacht? Ansonsten habe ich noch ein kleineres Compile-Problem gerade, was=20 irgendwie nicht sehr verst=E4ndlich ist. Ich hab bei dem=20 Vergleichsoperator noch einen Vergleich eingebaut um nach e-Value zu=20 sortieren, siehe unten. Dazu bekomme ich: razers_withBlast.h:631: error: `.' cannot appear in a constant- expression razers_withBlast.h:631: error: parse error in template argument list Danke! Gru=DF, Hannes template struct LessRNoGPos : public ::std::binary_function < TReadMatch,=20 TReadMatch, bool > { inline bool operator() (TReadMatch const &a, TReadMatch const &b)=20 const { // read number if (a.rseqNo < b.rseqNo) return true; if (a.rseqNo > b.rseqNo) return false; #ifdef RAZERS_BLAST // evalue if (a.eValue < b.eValue) return true; if (a.eValue > b.eValue) return false; #endif // genome position and orientation if (a.gseqNo < b.gseqNo) return true; if (a.gseqNo > b.gseqNo) return false; if (a.gBegin < b.gBegin) return true; if (a.gBegin > b.gBegin) return false; if (a.orientation < b.orientation) return true; if (a.orientation > b.orientation) return false; // quality #ifdef RAZERS_MATEPAIRS return a.pairScore > b.pairScore; #else return a.editDist < b.editDist; #endif } }; From Tobias.Rausch@fu-berlin.de Mon Aug 24 12:47:49 2009 Received: from outpost2.zedat.fu-berlin.de ([130.133.4.90]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1MfX5Y-0003yu-6g>; Mon, 24 Aug 2009 12:47:48 +0200 Received: from relay2.zedat.fu-berlin.de ([130.133.4.80]) by outpost1.zedat.fu-berlin.de (Exim 4.69) with esmtp (envelope-from ) id <1MfX5Y-0001JB-51>; Mon, 24 Aug 2009 12:47:48 +0200 Received: from exchange6.fu-berlin.de ([160.45.9.133]) by relay2.zedat.fu-berlin.de (Exim 4.69) with esmtp (envelope-from ) id <1MfX5Y-0004hP-13>; Mon, 24 Aug 2009 12:47:48 +0200 Received: from exchange6.fu-berlin.de ([160.45.9.133]) by exchange6.fu-berlin.de ([160.45.9.133]) with mapi; Mon, 24 Aug 2009 12:47:47 +0200 From: "Rausch, Tobias" To: "'andres.burgos@irisa.fr'" Date: Mon, 24 Aug 2009 12:47:47 +0200 Thread-Topic: [Seqan-dev] multiLocalAlignment function Thread-Index: AcokGsc1fXT6vnz5TqOgHXFNgT1lTAAjKomQ Message-ID: <6AB91D0276C1E744892C72E49C9DFFF7376A489A42@exchange6.fu-berlin.de> References: <4cdd147ccc281be49aabfc1f18b1245b.squirrel@mail.irisa.fr> <6AB91D0276C1E744892C72E49C9DFFF7376A5B2843@exchange6.fu-berlin.de> <70eafd2b63c4ffbd2457da559310d1bb.squirrel@mail.irisa.fr> In-Reply-To: <70eafd2b63c4ffbd2457da559310d1bb.squirrel@mail.irisa.fr> Accept-Language: en-US, de-DE Content-Language: de-DE X-MS-Has-Attach: X-MS-TNEF-Correlator: acceptlanguage: en-US, de-DE Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 X-Originating-IP: 160.45.9.133 X-purgate: clean X-purgate-ID: 151147::1251110868-000059FE-B3B7180B/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.044882, version=1.1.6 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Niger.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED Cc: "'seqan-dev@lists.fu-berlin.de'" Subject: Re: [Seqan-dev] multiLocalAlignment function X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Mon, 24 Aug 2009 10:47:49 -0000 Hi Andres, So here is an example: #include #include #include #include using namespace seqan; int main() { typedef String TSequence; TSequence seq1 =3D "atcgaatgcgga"; TSequence seq2 =3D "actcgttgca"; Score score(2, -1, -1, -2); typedef StringSet > TStringSet; TStringSet string_set; appendValue(string_set, seq1); appendValue(string_set, seq2); typedef String > TFragmentString; TFragmentString matches; typedef String TScoreValues; TScoreValues scores; multiLocalAlignment(string_set, matches, scores, score, 2, SmithWatermanCl= ump()); _debugMatches(string_set, matches); return 0; } It returns the two best local alignments as a string of fragments. The frag= ments are the gapless aligned segments of an alignment: 0,5,ATGC,1,5,TTGC 0,1,TCG,1,2,TCG The first number is the sequence id, then comes the begin position. So the = alignment is: TCGAAATGC TCG--TTGC The second local alignment is: 0,8,CG,1,3,CG 0,4,AAT,1,0,ACT The score string has the same length as the string of segment matches. Each= fragment gets the score of the local alignment it comes from. =20 I am not sure if this was already working in the last release, so please us= e the SVN. http://trac.mi.fu-berlin.de/seqan/wiki/Development Best regards, Tobias > -----Urspr=FCngliche Nachricht----- > Von: seqan-dev-bounces@lists.fu-berlin.de=20 > [mailto:seqan-dev-bounces@lists.fu-berlin.de] Im Auftrag von=20 > andres.burgos@irisa.fr > Gesendet: Sunday, August 23, 2009 7:55 PM > An: Rausch, Tobias > Cc: seqan-dev@lists.fu-berlin.de > Betreff: Re: [Seqan-dev] multiLocalAlignment function >=20 >=20 > Hi Tobias, thanks for your reply, I'll take a closer look at=20 > the code so maybe I'll figure it out, but the example will=20 > still be helpful. >=20 > Danke schoen! > Andres >=20 > > Hello Andres, > > > > The multi-local alignment algorithm we have implemented is the one=20 > > from Waterman and Eggert. > > It returns possibly overlapping local alignments, so it is not a=20 > > repeated match finder. > > > > It is implemented in > > ./seqan/graph_align/graph_align_smith_waterman_clump.h and=20 > as you can=20 > > see at the bottom of the file it repeatedly calls the standard=20 > > smith-waterman alignment algorithm. Each found local=20 > alignment is then=20 > > forbidden in the next run. > > > > I send you an example on how to use it on Monday. > > > > Best regards, > > Tobias > > > > > > ________________________________________ > > From: seqan-dev-bounces@lists.fu-berlin.de > > [seqan-dev-bounces@lists.fu-berlin.de] On Behalf Of=20 > > andres.burgos@irisa.fr [andres.burgos@irisa.fr] > > Sent: Friday, August 21, 2009 6:01 PM > > To: seqan-dev@lists.fu-berlin.de > > Subject: [Seqan-dev] multiLocalAlignment function > > > > Hi! > > > > I'm currently trying to make work the function > > > > multiLocalAlignment(graph, edgeMap, score, numAlign, tag) > > > > but I can't success, so I was hoping to get some help,=20 > since it's not=20 > > documented on the web site. I was also wondering weather=20 > this function=20 > > would return overlapping or non-overlapping alignments. > > > > Ok, so here is the code I'm working on: > > > > typedef seqan::String TString; > > typedef seqan::StringSet >=20 > TStringSet; > > typedef seqan::Graph > seqan::AminoAcid> > TGraph; > > > > TStringSet str; > > TString s1 ("some string"); > > TString s2 ("some other string"); > > > > seqan::appendValue(str, s1); > > seqan::appendValue(str, s2); > > > > seqan::Score > pam (250, -1, 0); > > TGraph g(str); > > > > =20 > seqan::String > int> > > propMap; > > seqan::resizeEdgeMap(g, propMap); > > > > seqan::multiLocalAlignment(g, propMap, pam, 10,=20 > > seqan::SmithWaterman()); > > > > This won't compile, throwing this error: > > > > ../seqan-1.1/seqan/graph_align/graph_align_interface.h: In function=20 > > 'void=20 > > seqan::multiLocalAlignment(seqan::Graph > TCargo, TSpec> >&, TPropertyMap&, const seqan::Score > TSpec2>&, TSize, TTag) [with TStringSet =3D > > seqan::StringSet > seqan::_AminoAcid>, seqan::Alloc >, seqan::Dependent > seqan::Tag > >, TCargo =3D=20 > > seqan::SimpleType, TSpec =3D const=20 > > seqan::Tag, TPropertyMap =3D=20 > > seqan::String > char>, seqan::StorePointsOnly>, seqan::Alloc >, TScoreValue =3D=20 > > int, TSpec2 =3D seqan::Pam > seqan::_AminoAcid>, seqan::Pam_Data_Dayhoff_MDM78>, TSize =3D=20 > int, TTag=20 > > =3D > > seqan::Tag]': > > readers/SWReader.cc:26: instantiated from here > > ../seqan-1.1/seqan/graph_align/graph_align_interface.h:234:=20 > error: no=20 > > matching function for call to=20 > > '_localAlignment(seqan::String > seqan::ExactFragment > >,=20 > > seqan::Alloc >&,=20 > > seqan::StringSet > seqan::_AminoAcid>, seqan::Alloc >, seqan::Dependent > seqan::Tag > >&,=20 > > seqan::String > char>, seqan::StorePointsOnly>, seqan::Alloc >&, const=20 > > seqan::Score > seqan::_AminoAcid>, seqan::Pam_Data_Dayhoff_MDM78> >&, int&,=20 > > seqan::Tag)' > > make: *** [readers/SWReader.o] Error 1 > > > > So, maybe an example would make things clearer... > > > > Thanks in advance, > > Andres > > > > > > _______________________________________________ > > seqan-dev mailing list > > seqan-dev@lists.fu-berlin.de > > https://lists.fu-berlin.de/listinfo/seqan-dev > > >=20 >=20 >=20 > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev > = From weese@inf.fu-berlin.de Mon Aug 24 12:55:10 2009 Received: from outpost2.zedat.fu-berlin.de ([130.133.4.90]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1MfXCe-0004DE-Nj>; Mon, 24 Aug 2009 12:55:08 +0200 Received: from inpost2.zedat.fu-berlin.de ([130.133.4.69]) by outpost1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1MfXCe-00030F-Lt>; Mon, 24 Aug 2009 12:55:08 +0200 Received: from [160.45.118.25] (helo=blowfish.mi.fu-berlin.de) by inpost2.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtpsa (envelope-from ) id <1MfXCe-0001ML-Iv>; Mon, 24 Aug 2009 12:55:08 +0200 Message-ID: <4A92718C.3090401@inf.fu-berlin.de> Date: Mon, 24 Aug 2009 12:55:08 +0200 From: David Weese User-Agent: Thunderbird 2.0.0.23 (Macintosh/20090812) MIME-Version: 1.0 To: SeqAn Development References: <200908231837.27473.hauswedell@mi.fu-berlin.de> <4A9259CB.7030708@inf.fu-berlin.de> <200908241158.10783.hauswedell@mi.fu-berlin.de> In-Reply-To: <200908241158.10783.hauswedell@mi.fu-berlin.de> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit X-Originating-IP: 160.45.118.25 X-purgate: clean X-purgate-ID: 151147::1251111308-000059FE-9AA06041/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.1.6 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Niger.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED Subject: Re: [Seqan-dev] Scoring mit Blosum62 X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Mon, 24 Aug 2009 10:55:10 -0000 Mmh, keine Ahnung. So seh ich noch nichts falsches. David > Ansonsten habe ich noch ein kleineres Compile-Problem gerade, was > irgendwie nicht sehr verst�ndlich ist. Ich hab bei dem > Vergleichsoperator noch einen Vergleich eingebaut um nach e-Value zu > sortieren, siehe unten. Dazu bekomme ich: > > razers_withBlast.h:631: error: `.' cannot appear in a constant- > expression > razers_withBlast.h:631: error: parse error in template argument list > > Danke! > > Gru�, > Hannes > > > > template > struct LessRNoGPos : public ::std::binary_function < TReadMatch, > TReadMatch, bool > > { > inline bool operator() (TReadMatch const &a, TReadMatch const &b) > const > { > // read number > if (a.rseqNo < b.rseqNo) return true; > if (a.rseqNo > b.rseqNo) return false; > > #ifdef RAZERS_BLAST > // evalue > if (a.eValue < b.eValue) return true; > if (a.eValue > b.eValue) return false; > #endif > // genome position and orientation > if (a.gseqNo < b.gseqNo) return true; > if (a.gseqNo > b.gseqNo) return false; > if (a.gBegin < b.gBegin) return true; > if (a.gBegin > b.gBegin) return false; > if (a.orientation < b.orientation) return true; > if (a.orientation > b.orientation) return false; > // quality > #ifdef RAZERS_MATEPAIRS > return a.pairScore > b.pairScore; > #else > return a.editDist < b.editDist; > #endif > } > }; > > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev > From andres.burgos@irisa.fr Tue Aug 25 14:34:11 2009 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1MfvE1-0007F4-6d>; Tue, 25 Aug 2009 14:34:09 +0200 Received: from mail4-relais-sop.national.inria.fr ([192.134.164.105]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1MfvE0-00010v-P3>; Tue, 25 Aug 2009 14:34:09 +0200 From: andres.burgos@irisa.fr X-IronPort-AV: E=Sophos;i="4.44,272,1249250400"; d="scan'208";a="45232325" Received: from omel.irisa.fr (HELO mail.irisa.fr) ([131.254.254.102]) by mail4-relais-sop.national.inria.fr with ESMTP; 25 Aug 2009 14:33:58 +0200 Received: from 131.254.10.65 (SquirrelMail authenticated user aburgos) by mail.irisa.fr with HTTP; Tue, 25 Aug 2009 14:34:01 +0200 Message-ID: In-Reply-To: <6AB91D0276C1E744892C72E49C9DFFF7376A489A42@exchange6.fu-berlin.de> References: <4cdd147ccc281be49aabfc1f18b1245b.squirrel@mail.irisa.fr> <6AB91D0276C1E744892C72E49C9DFFF7376A5B2843@exchange6.fu-berlin.de> <70eafd2b63c4ffbd2457da559310d1bb.squirrel@mail.irisa.fr> <6AB91D0276C1E744892C72E49C9DFFF7376A489A42@exchange6.fu-berlin.de> Date: Tue, 25 Aug 2009 14:34:01 +0200 To: "Rausch, Tobias" User-Agent: SquirrelMail/1.4.19 MIME-Version: 1.0 Content-Type: text/plain;charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Priority: 3 (Normal) Importance: Normal X-Originating-IP: 192.134.164.105 X-purgate: clean X-purgate-ID: 151147::1251203649-000059FE-082C20D9/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.1.6 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Niger.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=0.2 required=5.0 tests=NO_REAL_NAME Cc: "'seqan-dev@lists.fu-berlin.de'"