From matthias.dodt@mdc-berlin.de Thu Oct 01 10:36:37 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 <1MtH9Q-00078J-72>; Thu, 01 Oct 2009 10:36:36 +0200 Received: from sinope.bbbm.mdc-berlin.de ([141.80.25.23]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1MtH9Q-0004OL-56>; Thu, 01 Oct 2009 10:36:36 +0200 Received: from localhost (localhost [127.0.0.1]) by sinope.bbbm.mdc-berlin.de (Postfix) with ESMTP id BAE6C17C8EC for ; Thu, 1 Oct 2009 10:36:35 +0200 (CEST) X-Virus-Scanned: amavisd-new at mdc-berlin.de Received: from sinope.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (sinope.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 7jbuYom5+YRZ for ; Thu, 1 Oct 2009 10:36:29 +0200 (CEST) Received: from mdcmail.mdc-berlin.de (puck.citx.mdc-berlin.de [141.80.36.101]) by sinope.bbbm.mdc-berlin.de (Postfix) with ESMTP for ; Thu, 1 Oct 2009 10:36:29 +0200 (CEST) Received: from mdcexcl.mdc-berlin.net ([141.80.184.16]) by mdcmail.mdc-berlin.de with Microsoft SMTPSVC(6.0.3790.1830); Thu, 1 Oct 2009 10:36:29 +0200 Received: from cd04-macpro.local ([141.80.188.98]) by mdcexcl.mdc-berlin.net with Microsoft SMTPSVC(6.0.3790.3959); Thu, 1 Oct 2009 10:36:29 +0200 Message-ID: <4AC46A0C.2050200@mdc-berlin.de> Date: Thu, 01 Oct 2009 10:36:28 +0200 From: Matthias Dodt User-Agent: Thunderbird 2.0.0.23 (Macintosh/20090812) MIME-Version: 1.0 To: seqan-dev@lists.fu-berlin.de Content-Type: text/plain; charset=ISO-8859-15; format=flowed Content-Transfer-Encoding: 7bit X-OriginalArrivalTime: 01 Oct 2009 08:36:29.0029 (UTC) FILETIME=[45539150:01CA4272] X-TM-AS-Product-Ver: SMEX-8.0.0.1181-5.600.1016-16920.002 X-TM-AS-Result: No--4.720400-0.000000-31 X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-Originating-IP: 141.80.25.23 X-purgate: clean X-purgate-ID: 151147::1254386196-00000A7C-9C7F19B8/0-0/0-0 X-Bogosity: Unsure, tests=bogofilter, spamicity=0.493443, 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 X-Spam-Status: No, score=1.5 required=5.0 tests=FU_BOGO_UNSURE Subject: [Seqan-dev] file handling+fastq 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: Thu, 01 Oct 2009 08:36:37 -0000 Hi seqan users! I am having some problems using the readMeta and read commands. I think the documentation might be outdated... - the read(...) command hasnt a signature: read(file,data,meta,format) like indicated in the docs (it doesnt support meta) - the readMeta function doesnt support fastq - the guessFileformat() doesnt seem to work... Is it possible to read fastq metainformation with build-in functions? Thanks! Greetings mat From tzuchien.chiu@gmail.com Thu Oct 22 18:24:05 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 <1N10SK-0006hI-C8>; Thu, 22 Oct 2009 18:24:04 +0200 Received: from mail-fx0-f205.google.com ([209.85.220.205]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1N10SK-0003ri-9s>; Thu, 22 Oct 2009 18:24:04 +0200 Received: by fxm1 with SMTP id 1so11026501fxm.31 for ; Thu, 22 Oct 2009 09:24:04 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=gamma; h=domainkey-signature:mime-version:sender:received:date :x-google-sender-auth:message-id:subject:from:to:content-type; bh=HJzTFay9mUh5P3cqF16HOj2Cj85goZhn2IlSAXmJERQ=; b=qb45KztYCM/aADZKbn2vgxwotn/NoolyTV+1LRH79fs9DSLRLGedyqKaqFAjs3Vgu5 SvwLw5AFCer/+RS9OEM/8ouLONumCymHQco+0+R47Kwy02DY1l7C4Z3E7FYaQhcxyvke IoCGAGbQ6qcgI7KHeORUHhu983/NBlisMQZ5w= DomainKey-Signature: a=rsa-sha1; c=nofws; d=gmail.com; s=gamma; h=mime-version:sender:date:x-google-sender-auth:message-id:subject :from:to:content-type; b=ias2a/kFkYRz3HxLaOEuvnJbAsqrQswgM3foyy3LWOAaGrDph8ysokSnachhxcrRme FNbjjPsW1j1ufAenWt/i4sj0CCQkJCLE4s/4uiRu+mrgv0M4EVlo5O619RPZD7hAd86r 7n9rsdlT9rz/sxSHqiYrc3R1z22VwHN0PX434= MIME-Version: 1.0 Sender: tzuchien.chiu@gmail.com Received: by 10.204.26.206 with SMTP id f14mr9845018bkc.95.1256228643839; Thu, 22 Oct 2009 09:24:03 -0700 (PDT) Date: Thu, 22 Oct 2009 18:24:03 +0200 X-Google-Sender-Auth: ce6a7d91c2dc9f05 Message-ID: <4d77c5f20910220924w1cb1a83bx9e1e33e4e3c20a60@mail.gmail.com> From: Alex To: seqan-dev@lists.fu-berlin.de Content-Type: text/plain; charset=ISO-8859-1 X-Originating-IP: 209.85.220.205 X-purgate: clean X-purgate-ID: 151147::1256228644-00000DDD-F43FCDC6/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.211770, 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 X-Spam-Status: No, score=1.4 required=5.0 tests=DNS_FROM_RFC_POST, RCVD_BY_IP, SPF_HELO_PASS,SPF_PASS Subject: [Seqan-dev] Occurrences the longest matched needle 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: Thu, 22 Oct 2009 16:24:05 -0000 I want to count the number of longest matched substring in a sequence. For example, typedef String TSequence; typedef StringSet TStringSet TSequence haystack = "foo vino tinto bar"; StringSet needles; appendValue(needles, "vino"); appendValue(needles, "vino tinto"); Finder finder(haystack); Pattern pattern(needles); unsigned occurrences = 0; while (find(finder, pattern)) occurrences ++; In this case, occurrences is 2, since "vino" and "vino tinto" both match the haystack. But I only want to count the occurrences of the longest matches - "vino tinto". I cannot remove the needle "vino" since I also want to match the haystack "foo vino bar". From j.reid@mail.cryst.bbk.ac.uk Wed Oct 28 23:04:43 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 <1N3GdF-0007iG-Uv>; Wed, 28 Oct 2009 23:04:42 +0100 Received: from adora-ext.cryst.bbk.ac.uk ([193.61.32.13] helo=adora.cryst.bbk.ac.uk) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1N3GdF-0002c6-R3>; Wed, 28 Oct 2009 23:04:41 +0100 Received: from [127.0.0.1] (axon-ext.cryst.bbk.ac.uk [193.61.32.77]) by adora.cryst.bbk.ac.uk (8.13.8/8.13.8) with ESMTP id n9SMAN25016639 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NO) for ; Wed, 28 Oct 2009 22:10:25 GMT Message-ID: <4AE8BFF3.5080504@mail.cryst.bbk.ac.uk> Date: Wed, 28 Oct 2009 22:04:35 +0000 From: John Reid User-Agent: Thunderbird 2.0.0.23 (X11/20090817) MIME-Version: 1.0 To: seqan-dev@lists.fu-berlin.de Content-Type: text/plain; charset=windows-1252; format=flowed Content-Transfer-Encoding: 8bit X-Cryst-BBK-MailScanner-Information: Please contact CCSG for more information (http://www. cryst.bbk.ac.uk/CCSG) X-Cryst-BBK-MailScanner-ID: n9SMAN25016639 X-Cryst-BBK-MailScanner: Found to be clean X-Cryst-BBK-MailScanner-SpamCheck: not spam, SpamAssassin (not cached, score=0, required 5, autolearn=not spam) X-Cryst-BBK-MailScanner-From: j.reid@mail.cryst.bbk.ac.uk X-Cryst-BBK-MailScanner-Watermark: 1257372626.78664@ZYGuTGFESCRoCw3zoF+ayA X-Originating-IP: 193.61.32.13 X-purgate: clean X-purgate-ID: 151147::1256767481-00000DDD-AA282A55/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.061607, 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=0.4 required=5.0 tests=DNS_FROM_RFC_ABUSE, SPF_HELO_PASS,SPF_PASS Subject: [Seqan-dev] Problem with Markov Model and creating ticket on trac 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: Wed, 28 Oct 2009 22:04:43 -0000 Hi, I tried to create a new ticket on the seqan trac and got the following error: ProgrammingError: (1146, "Table 'seqan.spamfilter_log' doesn't exist") This was the content of the ticket I was trying to raise: I'm using the latest svn version of seqan (rev 4975) on ubuntu with gcc 4.3.3 and I'm getting a compilation error when I try to build a Markov model. As far as I can see the code below should work. Could you let me know if I'm doing something wrong or if this is a bug? {{{ #include #include using namespace seqan; int main() { MarkovModel< Dna > mm( 0 ); StringSet< String< Dna > > X; mm.build( X ); return 0; } }}} I get the following error: {{{ /home/john/Dev/ThirdParty/C++/seqan-svn/projects/library/seqan/statistical_index/statistical_index_markov_model.h: In member function ‘void seqan::MarkovModel< seqan::SimpleType, double, const seqan::Tag >::_computeAuxiliaryMatrices()’: /home/john/Dev/ThirdParty/C++/seqan-svn/projects/library/seqan/statistical_index/statistical_index_markov_model.h:180: instantiated from ‘void seqan::MarkovModel< seqan::SimpleType, double, const seqan::Tag >::build(seqan::StringSet, seqan::Alloc >, seqan::Owner > > &)’ src/sandbox/seqan_sandbox_markov_model.cpp:14: instantiated from here /home/john/Dev/ThirdParty/C++/seqan-svn/projects/library/seqan/statistical_index/statistical_index_markov_model.h:399: error: No match for ‘_matricialSum( seqan::String >, seqan::String > &, const unsigned int &)’ /home/john/Dev/ThirdParty/C++/seqan-svn/projects/library/seqan/statistical_index/statistical_index_markov_model.h:521: candidates are: seqan::String< TValue, seqan::Alloc > seqan::_matricialSum(seqan::String &, seqan::String &, unsigned int) /home/john/Dev/ThirdParty/C++/seqan-svn/projects/library/seqan/statistical_index/statistical_index_markov_model.h:402: error: No match for ‘_matricialProduct( seqan::String >, seqan::String > &, const unsigned int &)’ /home/john/Dev/ThirdParty/C++/seqan-svn/projects/library/seqan/statistical_index/statistical_index_markov_model.h:485: candidates are: seqan::String > seqan ::_matricialProduct(seqan::String &, seqan::String &, unsigned int) }}} From j.reid@mail.cryst.bbk.ac.uk Thu Oct 29 10:25:15 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 <1N3RFr-0002h1-0y>; Thu, 29 Oct 2009 10:25:15 +0100 Received: from adora-ext.cryst.bbk.ac.uk ([193.61.32.13] helo=adora.cryst.bbk.ac.uk) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1N3RFq-0008J0-TN>; Thu, 29 Oct 2009 10:25:15 +0100 Received: from [127.0.0.1] (axon-ext.cryst.bbk.ac.uk [193.61.32.77]) by adora.cryst.bbk.ac.uk (8.13.8/8.13.8) with ESMTP id n9T9UxrA001462 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NO) for ; Thu, 29 Oct 2009 09:31:01 GMT Message-ID: <4AE95F74.8040806@mail.cryst.bbk.ac.uk> Date: Thu, 29 Oct 2009 09:25:08 +0000 From: John Reid User-Agent: Thunderbird 2.0.0.23 (X11/20090817) MIME-Version: 1.0 To: seqan-dev@lists.fu-berlin.de Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Cryst-BBK-MailScanner-Information: Please contact CCSG for more information (http://www. cryst.bbk.ac.uk/CCSG) X-Cryst-BBK-MailScanner-ID: n9T9UxrA001462 X-Cryst-BBK-MailScanner: Found to be clean X-Cryst-BBK-MailScanner-SpamCheck: not spam, SpamAssassin (not cached, score=0, required 5, autolearn=not spam) X-Cryst-BBK-MailScanner-From: j.reid@mail.cryst.bbk.ac.uk X-Cryst-BBK-MailScanner-Watermark: 1257413461.93078@DN0+ULabM+y8j9wx6mGSig X-Originating-IP: 193.61.32.13 X-purgate: clean X-purgate-ID: 151147::1256808315-00000DDD-0436B51E/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.275153, 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=0.4 required=5.0 tests=DNS_FROM_RFC_ABUSE, SPF_HELO_PASS,SPF_PASS Subject: [Seqan-dev] MarkovModel 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: Thu, 29 Oct 2009 09:25:16 -0000 I don't think it is possible to calculate the emitted probability for a segment using a Markov model. There are only 2 overloads of emittedProbability (for Strings and StringSets). Would it be possible to add an overload for Segments? Thanks, John. From weese@campus.fu-berlin.de Sat Oct 31 10:10:38 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 <1N49yn-000139-7L>; Sat, 31 Oct 2009 10:10:37 +0100 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 <1N49yn-0004gQ-61>; Sat, 31 Oct 2009 10:10:37 +0100 Received: from [78.52.224.199] (helo=[192.168.100.30]) by inpost2.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtpsa (envelope-from ) id <1N49yn-0007NI-2t>; Sat, 31 Oct 2009 10:10:37 +0100 From: David Weese To: SeqAn Development In-Reply-To: <4AE95F74.8040806@mail.cryst.bbk.ac.uk> References: <4AE95F74.8040806@mail.cryst.bbk.ac.uk> Content-Type: text/plain; charset="UTF-8" Date: Sat, 31 Oct 2009 10:10:36 +0100 Message-ID: <1256980236.2434.23.camel@HAL.home> Mime-Version: 1.0 X-Mailer: Evolution 2.28.1 Content-Transfer-Encoding: 7bit X-Originating-IP: 78.52.224.199 X-purgate: clean X-purgate-ID: 151147::1256980237-00000DDD-71B830A7/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000269, 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 X-Mailman-Approved-At: Sat, 31 Oct 2009 19:52:14 +0100 Subject: Re: [Seqan-dev] MarkovModel 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: Sat, 31 Oct 2009 09:10:38 -0000 Hi John, you are absolutely right. I fixed that. Just make an SVN update. I reported the Trac problem to our admins. Ciao, Dave Am Donnerstag, den 29.10.2009, 10:25 +0100 schrieb John Reid: > I don't think it is possible to calculate the emitted probability for a > segment using a Markov model. There are only 2 overloads of > emittedProbability (for Strings and StringSets). Would it be possible to > add an overload for Segments? > > Thanks, > John. > > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev