From pjr314@gmail.com Fri Nov 04 02:10:57 2011 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 <1RM8J6-0006rc-M7>; Fri, 04 Nov 2011 02:10:56 +0100 Received: from mail-wy0-f182.google.com ([74.125.82.182]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1RM8J6-0004B5-IX>; Fri, 04 Nov 2011 02:10:56 +0100 Received: by wyg36 with SMTP id 36so2506836wyg.13 for ; Thu, 03 Nov 2011 18:10:56 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=gamma; h=mime-version:sender:date:x-google-sender-auth:message-id:subject :from:to:content-type; bh=5HE52gPd9nADEwEis2pBrcM3/PeCJ332qZgj4sY9dqQ=; b=Nw3BTLbyGcQ2kAVkvNwUH+dLAeD18KPFt6mJF4SeKGWmLL+Mw/hUrq+HNgFlMt3YD1 WMV0cl6zOMlEU909I6VJ2df9EYhojby29LPb5dg59cRIXzcBYeN/tMcn2eCcwRim5Vv2 8ZuxMD/wEIP+SN8py2yUZeZBLMXgKHdjx48Ao= MIME-Version: 1.0 Received: by 10.216.134.5 with SMTP id r5mr2545246wei.12.1320369056047; Thu, 03 Nov 2011 18:10:56 -0700 (PDT) Sender: pjr314@gmail.com Received: by 10.216.171.5 with HTTP; Thu, 3 Nov 2011 18:10:55 -0700 (PDT) Date: Thu, 3 Nov 2011 20:10:55 -0500 X-Google-Sender-Auth: EEPinF9iWj_9blqfnD1d2QaJPxs Message-ID: From: patrick reed To: seqan-dev@lists.fu-berlin.de Content-Type: multipart/alternative; boundary=0016e6d77cfe8ee47f04b0de60e5 X-Originating-IP: 74.125.82.182 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1320369056-00004510-91B03179/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.212403, version=1.2.2 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=0.5 required=5.0 tests=DNS_FROM_RFC_ABUSE, HTML_00_10, HTML_MESSAGE,RCVD_BY_IP,SPF_HELO_PASS,SPF_PASS Subject: [Seqan-dev] reference genome size limitation 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: Fri, 04 Nov 2011 01:10:57 -0000 --0016e6d77cfe8ee47f04b0de60e5 Content-Type: text/plain; charset=ISO-8859-1 Hi, I am trying to use tophat/bowtie to allign RNAseq data to a reference genome that is about 7gb in size. From what i can decipher from your internals, i am a c++ novice, they use your software in the build functionality to build a reference genome, and SeqAn uses 32bit integers which limits the maximum reference size to about 4gb. Is there anyway to convert to 64bit integers to allow for an extremely large reference genome. -- Patrick Reed Graduate Student White Lab, IGSB Committee on Neurobiology University of Chicago 773-490-6241 This email is intended only for the use of the individual or entity to which it is addressed and may contain information that is privileged and confidential. If the reader of this email message is not the intended recipient, you are hereby notified that any dissemination, distribution, or copying of this communication is prohibited. If you have received this email in error, please notify the sender and destroy/delete all copies of the transmittal. Thank you. --0016e6d77cfe8ee47f04b0de60e5 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi, I am trying to use tophat/bowtie to allign RNAseq data to a reference g= enome that is about 7gb in size. =A0From what i can decipher from your inte= rnals, i am a c++ novice, they use your software in the build functionality= to build a reference genome, and SeqAn uses 32bit integers which limits th= e maximum reference size to about 4gb. =A0Is there anyway to convert to 64b= it integers to allow for an=A0extremely=A0large reference genome.

--
Patrick Reed
Graduate Student
White Lab, IGSBCommittee on Neurobiology
University of Chicago
773-490-6241





This email is intended only for the use of the indivi= dual or entity to which it is addressed and may contain information that is= privileged and confidential. If the reader of this email message is not th= e intended recipient, you are hereby notified that any dissemination, distr= ibution, or copying of this communication is prohibited. If you have receiv= ed this email in error, please notify the sender and destroy/delete all cop= ies of the transmittal. Thank you.

--0016e6d77cfe8ee47f04b0de60e5-- From manuel.holtgrewe@fu-berlin.de Fri Nov 04 08:14:11 2011 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 <1RMDyc-00041V-9S>; Fri, 04 Nov 2011 08:14:10 +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 <1RMDyc-0001jB-7P>; Fri, 04 Nov 2011 08:14:10 +0100 Received: from 91-65-212-104-dynip.superkabel.de ([91.65.212.104] helo=[192.168.0.100]) by inpost2.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtpsa (envelope-from ) id <1RMDyc-0001YJ-4t>; Fri, 04 Nov 2011 08:14:10 +0100 Message-ID: <4EB390C1.6010601@fu-berlin.de> Date: Fri, 04 Nov 2011 08:14:09 +0100 From: Manuel Holtgrewe User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:7.0.1) Gecko/20110929 Thunderbird/7.0.1 MIME-Version: 1.0 To: SeqAn Development References: In-Reply-To: Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Originating-IP: 91.65.212.104 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1320390850-00004510-8AA60E01/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000003, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Algerien.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=-2.0 required=5.0 tests=ALL_TRUSTED, RATWARE_GECKO_BUILD Subject: Re: [Seqan-dev] reference genome size limitation 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: Fri, 04 Nov 2011 07:14:11 -0000 On 04.11.2011 02:10, patrick reed wrote: > Hi, I am trying to use tophat/bowtie to allign RNAseq data to a > reference genome that is about 7gb in size. From what i can decipher > from your internals, i am a c++ novice, they use your software in the > build functionality to build a reference genome, and SeqAn uses 32bit > integers which limits the maximum reference size to about 4gb. Is there > anyway to convert to 64bit integers to allow for an extremely large > reference genome. Dear Patrick, can you give me a link (file/lines) in the tophead/bowtie download ZIP file that you think causes the problem? SeqAn is very generic in this aspect and Strings can be configured to either use 32 bit (to save memory in pointers/locations) or 64 bit addresses (to give you virtually unlimited addressable memory). We have successfully used SeqAn Strings of more than 4GB and indices on them. It might be that the tophead/bowtie authors used the String class such that only 32 bit pointers were used (intentionally or unintentionally) or that they triggered a bug in SeqAn that we are not aware of. We might be able to help in the first case and will be in the second. Bests, Manuel From Birte.Kehr@fu-berlin.de Tue Nov 08 00:50:50 2011 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 <1RNYxl-0000Sl-OJ>; Tue, 08 Nov 2011 00:50:49 +0100 Received: from relay2.zedat.fu-berlin.de ([130.133.4.80]) by outpost1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1RNYxl-0003tZ-LB>; Tue, 08 Nov 2011 00:50:49 +0100 Received: from exchange6.fu-berlin.de ([160.45.9.133]) by relay2.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1RNYxl-0003b3-F0>; Tue, 08 Nov 2011 00:50:49 +0100 Received: from exchange6.fu-berlin.de ([160.45.9.133]) by exchange6.fu-berlin.de ([160.45.9.133]) with mapi; Tue, 8 Nov 2011 00:50:49 +0100 From: "Kehr, Birte" To: SeqAn Development Date: Tue, 8 Nov 2011 00:50:47 +0100 Thread-Topic: [Seqan-dev] about extendSeed of Seqan Thread-Index: AcydphrTNwwsgndPQzGFFdC4h8fWnwAARedA Message-ID: 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: multipart/alternative; boundary="_000_DAD226CB6878494EABEFD5215AA102015A9527EA5Fexchange6fube_" MIME-Version: 1.0 X-Originating-IP: 160.45.9.133 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1320709849-000067B8-8B9FAD2B/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.2.2 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=-2.8 required=5.0 tests=ALL_TRUSTED,HTML_MESSAGE Subject: [Seqan-dev] FW: about extendSeed of Seqan 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, 07 Nov 2011 23:50:50 -0000 --_000_DAD226CB6878494EABEFD5215AA102015A9527EA5Fexchange6fube_ Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Could anyone help Beifang with the question below? Thanks, Birte From: Beifang Niu [mailto:neilniu.cn@gmail.com] Sent: Montag, 7. November 2011 15:37 To: Kehr, Birte Subject: Re: [Seqan-dev] about extendSeed of Seqan Hi Birte, Now I have a new question for you. There is one example for DNA seed extension in the seqan tutorial. If I wan= t to do the seed extension for protein sequences using blosum 62 scoring ma= trix. How to do it? Can I directly use extendSeed function? It seems that the s= core parameter of the extendSeed function is simple score type. Can I use b= losum 62 scoring matrix for extendSeed function? thank you, Beifang. --_000_DAD226CB6878494EABEFD5215AA102015A9527EA5Fexchange6fube_ Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Could anyone help Beifang with the question below?

<= p class=3DMsoNormal>Thanks, Birte

=

 

 

<= p class=3DMsoNormal>From: Beifang Niu [mailto:neiln= iu.cn@gmail.com]
Sent: Montag, 7. November 2011 15:37
To:<= /b> Kehr, Birte
Subject: Re: [Seqan-dev] about extendSeed of Seqa= n

 

Hi Birte,

&nb= sp;

Now I have a new question for = you.

There is one example for= DNA seed extension in the seqan tutorial. If I want to do the seed extensi= on for protein sequences using blosum 62 scoring matrix. 

How to do it?  Can I directly u= se extendSeed function?  It seems that the score parameter of the exte= ndSeed function is simple score type. Can I use blosum 62 scoring matrix fo= r extendSeed function?

&= nbsp;

thank you,

Beifang.

= --_000_DAD226CB6878494EABEFD5215AA102015A9527EA5Fexchange6fube_-- From neilniu.cn@gmail.com Tue Nov 08 01:54:17 2011 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 <1RNZxA-0002nT-Pk>; Tue, 08 Nov 2011 01:54:16 +0100 Received: from mail-qw0-f54.google.com ([209.85.216.54]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1RNZxA-0002jW-JD>; Tue, 08 Nov 2011 01:54:16 +0100 Received: by qadb12 with SMTP id b12so3471692qad.13 for ; Mon, 07 Nov 2011 16:54:15 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=gamma; h=mime-version:date:message-id:subject:from:to:content-type; bh=FkfF82yFbCWRF+6gPjxXzUBSCvKMgdfH8wVx/hqDpnQ=; b=AOMOzD+0fp6pAJ9jV41Q9DGVSQa5e6SGJT6mj2Qgjm+lK5Nlh8WkTiJgnecJsrhoSf tX25ElePmZCSMsdcUOVbCDRt1C8cdQYwx503FtVjsPsKxkBmt+emRZFvYOIhqgvyu1J3 QIRDgCIxvEtptb676bF03pc8yeyftbZEQiGmM= MIME-Version: 1.0 Received: by 10.224.186.8 with SMTP id cq8mr13805539qab.45.1320713655665; Mon, 07 Nov 2011 16:54:15 -0800 (PST) Received: by 10.224.86.11 with HTTP; Mon, 7 Nov 2011 16:54:15 -0800 (PST) Date: Mon, 7 Nov 2011 16:54:15 -0800 Message-ID: From: Beifang Niu To: seqan-dev@lists.fu-berlin.de Content-Type: multipart/alternative; boundary=20cf30334f294bc4fc04b12e9caa X-Originating-IP: 209.85.216.54 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1320713656-000067B8-62AA47A8/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.020794, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Burundi.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=0.4 required=5.0 tests=DNS_FROM_RFC_ABUSE, HTML_60_70, HTML_MESSAGE,RCVD_BY_IP,SPF_HELO_PASS,SPF_PASS Subject: [Seqan-dev] extendSeed for protein sequences 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: Tue, 08 Nov 2011 00:54:17 -0000 --20cf30334f294bc4fc04b12e9caa Content-Type: text/plain; charset=ISO-8859-1 Hi all, There is one example for DNA seed extension in the seqan tutorial. If I want to do the seed extension for protein sequences using blosum 62 scoring matrix. How to do it? Can I directly use extendSeed function? It seems that the score parameter of the extendSeed function is simple score type. Can I use blosum 62 scoring matrix for extendSeed function? thank you, Beifang. --20cf30334f294bc4fc04b12e9caa Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi all,

There is one example for DNA seed extension in the seqan tut= orial. If I want to do the seed extension for protein sequences=A0using blo= sum 62 scoring matrix.=A0
How to do it= ? =A0Can I directly use extendSeed function? =A0It seems that the score par= ameter of the extendSeed function is simple score type. Can I use blosum 62= scoring matrix for extendSeed function?

thank you,
Beifang.
--20cf30334f294bc4fc04b12e9caa-- From manuel.holtgrewe@fu-berlin.de Tue Nov 08 09:42:55 2011 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 <1RNhGg-0004Hm-6K>; Tue, 08 Nov 2011 09:42:54 +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 <1RNhGg-0007Ux-4K>; Tue, 08 Nov 2011 09:42:54 +0100 Received: from 91-65-212-104-dynip.superkabel.de ([91.65.212.104] helo=[192.168.0.100]) by inpost2.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtpsa (envelope-from ) id <1RNhGg-0006cE-1c>; Tue, 08 Nov 2011 09:42:54 +0100 Message-ID: <4EB8EB8D.3040604@fu-berlin.de> Date: Tue, 08 Nov 2011 09:42:53 +0100 From: Manuel Holtgrewe User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:7.0.1) Gecko/20110929 Thunderbird/7.0.1 MIME-Version: 1.0 To: SeqAn Development References: In-Reply-To: Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Originating-IP: 91.65.212.104 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1320741774-000067B8-D4D342AA/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000030, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Algerien.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=-2.0 required=5.0 tests=ALL_TRUSTED, RATWARE_GECKO_BUILD Subject: Re: [Seqan-dev] extendSeed for protein sequences 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: Tue, 08 Nov 2011 08:42:55 -0000 On 08.11.2011 01:54, Beifang Niu wrote: > Hi all, > > There is one example for DNA seed extension in the seqan tutorial. If I > want to do the seed extension for protein sequences using blosum 62 > scoring matrix. > How to do it? Can I directly use extendSeed function? It seems that > the score parameter of the extendSeed function is simple score type. Can > I use blosum 62 scoring matrix for extendSeed function? > > thank you, > Beifang. Beifang, the tutorial gives the following for using simple score matrices: typedef int TScore; Score scoreMatrix(1, -1, -1); TScore scoreDropOff = 1; extendSeed(seed, scoreDropOff, scoreMatrix, seq0, seq1, 2, GappedXDrop()); The alignment tutorial [1] explains how to use the built-in Blosum 62. You can also find Blosum62, other Blosums, Pams and Vtml200 in the documentation. You probably want to do the following: typedef int TScore; TScore gapExtend = -1, gapOpen = -11; Blosum62 scoringScheme(gapExtend/* optional:, gapOpen*/); extendSeed(seed, scoreDropOff, scoreMatrix, seq0, seq1, 2, GappedXDrop()); Finally, the How-To [2] shows how to define your own score matrices. I hope that this helps you. Can you tell us how we could improve the documentation such that you could have found this information faster? By the way, the Tutorial site has a search function ;) Bests, Manuel [1] http://trac.mi.fu-berlin.de/seqan/wiki/Tutorial/Alignments [2] http://trac.mi.fu-berlin.de/seqan/wiki/HowTo/WorkWithCustomScoreMatrices From neilniu.cn@gmail.com Tue Nov 08 20:38:10 2011 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 <1RNrUn-0006xF-Hb>; Tue, 08 Nov 2011 20:38:09 +0100 Received: from mail-qw0-f47.google.com ([209.85.216.47]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1RNrUn-0005Ic-82>; Tue, 08 Nov 2011 20:38:09 +0100 Received: by qabj40 with SMTP id j40so937742qab.13 for ; Tue, 08 Nov 2011 11:38:08 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=gamma; h=mime-version:in-reply-to:references:date:message-id:subject:from:to :content-type; bh=qxhYH9bjCeqKBI820kuT+EIivQyKCd1wJiZPkrYIt60=; b=W3lgPXxalMoy+JAnnsyr7YuZ2fgOLfIXWqipBv8CciwrKFEUzu3xpi/VGajM8DXCO7 3gemYnxZIWi1dytRLXGaL0062dflYqbC1YNy6Gfs22k8YzTmuvfSTYE+oIWbSAEcpW3V dxmt2TrorRHlcqefZgVzIKCvlIHJv0fBB2o2o= MIME-Version: 1.0 Received: by 10.224.217.74 with SMTP id hl10mr16005910qab.84.1320781086845; Tue, 08 Nov 2011 11:38:06 -0800 (PST) Received: by 10.224.86.11 with HTTP; Tue, 8 Nov 2011 11:38:06 -0800 (PST) In-Reply-To: References: Date: Tue, 8 Nov 2011 11:38:06 -0800 Message-ID: From: Beifang Niu To: seqan-dev@lists.fu-berlin.de Content-Type: multipart/alternative; boundary=20cf300fb3c581ec2c04b13e4f49 X-Originating-IP: 209.85.216.47 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1320781089-000067B8-480D0EB2/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Botsuana.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=0.5 required=5.0 tests=DNS_FROM_RFC_ABUSE, HTML_30_40, HTML_MESSAGE,RCVD_BY_IP,SPF_HELO_PASS,SPF_PASS Subject: Re: [Seqan-dev] seqan-dev Digest, Vol 26, Issue 2 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: Tue, 08 Nov 2011 19:38:10 -0000 --20cf300fb3c581ec2c04b13e4f49 Content-Type: text/plain; charset=ISO-8859-1 Hi Manuel, I did read the documents and test extendSeed function for Blosum 62 but it seems that extendSeed function did not accept the scoring scheme of Blosum 62. I doubt that extendSeed accept only simple score scheme. the following is the test code: typedef int TScore; TScore gapExtend = -1, gapOpen = -11; Blosum62 scoringScheme(gapExtend, gapOpen); extendSeed(seed, scoreDropOff, scoringScheme, seq0, seq1, 2, GappedXDrop()); the compiling error message is : error: no matching function for call to 'extendSeed(main()::TSeed&, main::TScore&, seqan::Blosum62&, main()::TInfix&, main()::TInfix&, int, const seqan::GappedXDrop)' any ideas? thanks, On Tue, Nov 8, 2011 at 3:00 AM, wrote: > > On 08.11.2011 01:54, Beifang Niu wrote: > > Hi all, > > > > There is one example for DNA seed extension in the seqan tutorial. If I > > want to do the seed extension for protein sequences using blosum 62 > > scoring matrix. > > How to do it? Can I directly use extendSeed function? It seems that > > the score parameter of the extendSeed function is simple score type. Can > > I use blosum 62 scoring matrix for extendSeed function? > > > > thank you, > > Beifang. > Beifang, > > the tutorial gives the following for using simple score matrices: > > typedef int TScore; > Score scoreMatrix(1, -1, -1); > TScore scoreDropOff = 1; > extendSeed(seed, scoreDropOff, scoreMatrix, seq0, seq1, 2, > GappedXDrop()); > > The alignment tutorial [1] explains how to use the built-in Blosum 62. > You can also find Blosum62, other Blosums, Pams and Vtml200 in the > documentation. You probably want to do the following: > > typedef int TScore; > TScore gapExtend = -1, gapOpen = -11; > Blosum62 scoringScheme(gapExtend/* optional:, gapOpen*/); > extendSeed(seed, scoreDropOff, scoreMatrix, seq0, seq1, 2, > GappedXDrop()); > > Finally, the How-To [2] shows how to define your own score matrices. > > I hope that this helps you. Can you tell us how we could improve the > documentation such that you could have found this information faster? By > the way, the Tutorial site has a search function ;) > > Bests, > Manuel > > [1] http://trac.mi.fu-berlin.de/seqan/wiki/Tutorial/Alignments > [2] > http://trac.mi.fu-berlin.de/seqan/wiki/HowTo/WorkWithCustomScoreMatrices > > > > ------------------------------ > > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev > > > End of seqan-dev Digest, Vol 26, Issue 2 > **************************************** > --20cf300fb3c581ec2c04b13e4f49 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi Manuel,

I did read the documents and test extendSeed = function for Blosum 62 but it seems that extendSeed function did not accept= the scoring scheme of Blosum 62.=A0
I doubt that extendSeed acce= pt only simple score scheme.

the following is the test code:

=A0 =A0 typedef int TScore;
=A0 =A0 TScore gapExtend =3D -1, gapOpen = =3D -11;
=A0 =A0 Blosum62 scoringScheme(gapExtend, gapOpen);
=A0 =A0 = extendSeed(seed, scoreDropOff, scoringScheme, seq0, seq1, 2,=A0GappedXDrop(= ));

the compiling error message is :=A0

error: no matching function for call to 'extendSeed(main()::TSeed= &, main::TScore&, seqan::Blosum62&, main()::TInfix&, main()= ::TInfix&, int, const seqan::GappedXDrop)'

any ideas?=A0

thanks,


On Tue, Nov 8, 2011 at 3:00= AM, <seqan-dev-request@lists.fu-berlin.de> wrote:

On 08.11.2011 01:54, Beifang Niu wrote:
> Hi all,
>
> There is one example for DNA seed extension in the seqan tutorial. If = I
> want to do the seed extension for protein sequences using blosum 62 > scoring matrix.
> How to do it? =A0Can I directly use extendSeed function? =A0It seems t= hat
> the score parameter of the extendSeed function is simple score type. C= an
> I use blosum 62 scoring matrix for extendSeed function?
>
> thank you,
> Beifang.
Beifang,

the tutorial gives the following for using simple score matrices:

=A0 =A0 typedef int TScore;
=A0 =A0 Score<TScore, Simple> scoreMatrix(1, -1, -1);
=A0 =A0 TScore scoreDropOff =3D 1;
=A0 =A0 extendSeed(seed, scoreDropOff, scoreMatrix, seq0, seq1, 2,
GappedXDrop());

The alignment tutorial [1] explains how to use the built-in Blosum 62.
You can also find Blosum62, other Blosums, Pams and Vtml200 in the
documentation. You probably want to do the following:

=A0 =A0 typedef int TScore;
=A0 =A0 TScore gapExtend =3D -1, gapOpen =3D -11;
=A0 =A0 Blosum62 scoringScheme(gapExtend/* optional:, gapOpen*/);
=A0 =A0 extendSeed(seed, scoreDropOff, scoreMatrix, seq0, seq1, 2,
GappedXDrop());

Finally, the How-To [2] shows how to define your own score matrices.

I hope that this helps you. Can you tell us how we could improve the
documentation such that you could have found this information faster? By the way, the Tutorial site has a search function ;)

Bests,
Manuel

[1] http://trac.mi.fu-berlin.de/seqan/wiki/Tutorial/Alignment= s
[2] http://trac.mi.fu-berlin.de/seqan/wiki/HowT= o/WorkWithCustomScoreMatrices



------------------------------

_______________________________________________
seqan-dev mailing list
seqan-dev@lists.fu-berlin.d= e
https://lists.fu-berlin.de/listinfo/seqan-dev


End of seqan-dev Digest, Vol 26, Issue 2
****************************************

--20cf300fb3c581ec2c04b13e4f49-- From manuel.holtgrewe@fu-berlin.de Tue Nov 08 20:48:55 2011 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 <1RNrfC-0007Jk-Hn>; Tue, 08 Nov 2011 20:48:54 +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 <1RNrfC-0001et-Fv>; Tue, 08 Nov 2011 20:48:54 +0100 Received: from 91-65-212-104-dynip.superkabel.de ([91.65.212.104] helo=[192.168.0.100]) by inpost2.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtpsa (envelope-from ) id <1RNrfC-0007ge-DL>; Tue, 08 Nov 2011 20:48:54 +0100 Message-ID: <4EB987A6.6060907@fu-berlin.de> Date: Tue, 08 Nov 2011 20:48:54 +0100 From: Manuel Holtgrewe User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:7.0.1) Gecko/20110929 Thunderbird/7.0.1 MIME-Version: 1.0 To: SeqAn Development References: In-Reply-To: Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Originating-IP: 91.65.212.104 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1320781734-000067B8-57526F40/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Dschibuti.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=-2.0 required=5.0 tests=ALL_TRUSTED, RATWARE_GECKO_BUILD Subject: Re: [Seqan-dev] seqan-dev Digest, Vol 26, Issue 2 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: Tue, 08 Nov 2011 19:48:55 -0000 Beifang, are you using the seeds or the seeds2 module? *m From neilniu.cn@gmail.com Fri Nov 11 01:07:58 2011 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 <1ROeez-0001Ma-Gh>; Fri, 11 Nov 2011 01:07:57 +0100 Received: from mail-qw0-f47.google.com ([209.85.216.47]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1ROeez-00041r-AS>; Fri, 11 Nov 2011 01:07:57 +0100 Received: by qabj40 with SMTP id j40so3483537qab.13 for ; Thu, 10 Nov 2011 16:07:56 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=gamma; h=mime-version:date:message-id:subject:from:to:content-type; bh=OsqLvEaZXPWLd1k9m0IUBysP5qe5p8Zhm+2Fh8SkHoY=; b=hSARH587CDhKPA4PhC0xBgcgeoLvt1mheHLP8IiAOu5AsZPEF3XIckTutQNJZ3kSVU IT0BfyQo0Ais/V+6yWcHKX+4xVH88FOo1aOUBoYieqPSinBnru+hpNPefhSBZZyFX7Zj ViAAGOPVyVZmga5LzkdLrXzYy42qgjjzy7PAU= MIME-Version: 1.0 Received: by 10.224.217.74 with SMTP id hl10mr7652959qab.84.1320969728565; Thu, 10 Nov 2011 16:02:08 -0800 (PST) Received: by 10.224.86.11 with HTTP; Thu, 10 Nov 2011 16:02:08 -0800 (PST) Date: Thu, 10 Nov 2011 16:02:08 -0800 Message-ID: From: Beifang Niu To: seqan-dev@lists.fu-berlin.de Content-Type: multipart/alternative; boundary=20cf300fb3c56e22c704b16a3b9c X-Originating-IP: 209.85.216.47 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1320970077-000067B8-3623D035/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Dschibuti.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=0.9 required=5.0 tests=DNS_FROM_RFC_ABUSE, HTML_60_70, HTML_MESSAGE,HTML_OBFUSCATE_05_10,RCVD_BY_IP,SPF_HELO_PASS,SPF_PASS Subject: [Seqan-dev] about the best local alignment using BandedSmithWaterman 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: Fri, 11 Nov 2011 00:07:58 -0000 --20cf300fb3c56e22c704b16a3b9c Content-Type: text/plain; charset=ISO-8859-1 Hi Seqan, There is one function "localAlignment" in the Seqan tutorial. Are there only three tags " BandedWatermanEggert , SmithWaterman , WatermanEggert" ? I am wondering why there is no BandedSmithWaterman tag? If I want to computes the best local alignment of two sequences using banded smithWaterman algorithm with fixed band length (for example: band length = 10 ), Can I use LocalAlignment function to do that? I have another question about the alignments and seed extension in the Seqan library. It seems that there is no any parameter or return value for alignment identity ( matched base/ alignment length ) and the sequence identity of seed extension part (matched base / extension part length ). Although, users can parse the alignment results or rewrite the seed extension code to get the sequence identity, I still hope I can get sequence identity directly from alignments or seed extension results. thanks, Beifang --20cf300fb3c56e22c704b16a3b9c Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi Seqan,

There is one function "localAlignment" in the Seqan tutori= al.
Are there only three tags "=A0,=A0SmithWaterman,=A0WatermanEggert" ? =A0I am wondering why there= is no BandedSmithWaterman tag?

If I want to computes the best local alignment of two s= equences using banded smithWaterman algorithm with fixed band length (for e= xample: band length =3D 10 ), =A0Can I use LocalAlignment function to do th= at?

I have another question about the alignments and seed e= xtension in the Seqan library. =A0It seems that there is no any parameter o= r return value for alignment identity ( matched base/ alignment length ) an= d the sequence identity of seed extension part (matched base / extension pa= rt length ).
Although, users can parse the alignment results or rewrite the seed ex= tension code to get the sequence identity, =A0I still hope I can get sequen= ce identity directly from alignments or seed extension results.

thanks,
Beifang
--20cf300fb3c56e22c704b16a3b9c-- From manuel.holtgrewe@fu-berlin.de Fri Nov 11 14:22:56 2011 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 <1ROr4J-0001PJ-Hv>; Fri, 11 Nov 2011 14:22:55 +0100 Received: from inpost2.zedat.fu-berlin.de ([130.133.4.69]) by outpost1.zedat.fu-berlin.de (Exim 4.69) with esmtp (envelope-from ) id <1ROr4J-0003K1-Ey>; Fri, 11 Nov 2011 14:22:55 +0100 Received: from ecoli.imp.fu-berlin.de ([160.45.111.133]) by inpost2.zedat.fu-berlin.de (Exim 4.69) with esmtpsa (envelope-from ) id <1ROr4J-00045b-BR>; Fri, 11 Nov 2011 14:22:55 +0100 Message-ID: <4EBD219C.7080203@fu-berlin.de> Date: Fri, 11 Nov 2011 14:22:36 +0100 From: Manuel Holtgrewe User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:7.0.1) Gecko/20110929 Thunderbird/7.0.1 MIME-Version: 1.0 To: SeqAn Development References: In-Reply-To: Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Originating-IP: 160.45.111.133 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1321017775-000067B8-44B0426A/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Algerien.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=-2.0 required=5.0 tests=ALL_TRUSTED, RATWARE_GECKO_BUILD Subject: Re: [Seqan-dev] about the best local alignment using BandedSmithWaterman 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: Fri, 11 Nov 2011 13:22:56 -0000 Hi Beifang, On 11/11/2011 01:02 AM, Beifang Niu wrote: > Hi Seqan, > > There is one function "localAlignment" in the Seqan tutorial. > Are there only three tags "BandedWatermanEggert > , > SmithWaterman > , > WatermanEggert > " > ? I am wondering why there is no BandedSmithWaterman tag? > > If I want to computes the best local alignment of two sequences using > banded smithWaterman algorithm with fixed band length (for example: band > length = 10 ), Can I use LocalAlignment function to do that? There is a BandedSmithWaterman tag and there is a localAlignment() function for it. I'm no expert in this part of SeqAn, but you could have a look at the source in align/align_local_dynprog_banded.h and give it a try. > I have another question about the alignments and seed extension in the > Seqan library. It seems that there is no any parameter or return value > for alignment identity ( matched base/ alignment length ) and the > sequence identity of seed extension part (matched base / extension part > length ). > Although, users can parse the alignment results or rewrite the seed > extension code to get the sequence identity, I still hope I can get > sequence identity directly from alignments or seed extension results. I think the main problem here is how seeds work: The Simple Seed does not store any alignment information, it only consists of start/end coordinates in both sequences together with a score. It is not stored yet how any gaps look like. The Chained Seed stores lists of diagonals. However, we have not yet had much use for it in seeds2, so the extension algorithm has not been written for it yet. There is a comment in seeds2/seeds_extension.h (around line 730) that describes how this could be implemented. The main challenge here is that the extension algorithm itself only gives you a score and the new begin/end coordinates in the sequences. You would have to implement banded alignment and extract the matching diagonals from the alignment. When you are using Chained Seeds then a iteration over its diagonals can give you an alignment, sequence identity etc. etc. We would welcome a tested patch with this functionality. Bests, Manuel From rwan@cuhk.edu.hk Tue Nov 22 11:05:02 2011 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 <1RSnDo-0004VT-R1>; Tue, 22 Nov 2011 11:05:00 +0100 Received: from cmt1.itsc.cuhk.edu.hk ([137.189.11.91]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1RSnDo-0004PY-EB>; Tue, 22 Nov 2011 11:05:00 +0100 Received: from [192.168.129.108] (unknown [210.177.253.61]) (using TLSv1 with cipher AES256-SHA (256/256 bits)) (No client certificate requested) (Authenticated sender: b126594) by cmt1.itsc.cuhk.edu.hk (Postfix) with ESMTPSA id 91A3A8201CC for ; Tue, 22 Nov 2011 18:04:55 +0800 (HKT) Message-ID: <4ECB73C7.4040204@cuhk.edu.hk> Date: Tue, 22 Nov 2011 18:04:55 +0800 From: Raymond Wan User-Agent: Mozilla/5.0 (X11; U; Linux x86_64; en-US; rv:1.9.1.16) Gecko/20111110 Icedove/3.0.11 MIME-Version: 1.0 To: SeqAn Development Content-Type: text/plain; charset=UTF-8; format=flowed Content-Transfer-Encoding: 7bit X-Originating-IP: 137.189.11.91 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1321956300-000067B8-1379ADD2/0-0/0-0 X-Bogosity: Unsure, tests=bogofilter, spamicity=0.464525, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Algerien.ZEDAT.FU-Berlin.DE X-Spam-Level: xx X-Spam-Status: No, score=2.3 required=5.0 tests=FU_BOGO_UNSURE, RATWARE_GECKO_BUILD Subject: [Seqan-dev] RecordReader question 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: Tue, 22 Nov 2011 10:05:02 -0000 Dear all, Sorry if this is a silly question, but I'm trying to get the RecordReader example at: http://trac.mi.fu-berlin.de/seqan/browser/trunk/seqan/extras/demos/tutorial/stream/stream_read_record_fasta.cpp working but have been unsuccessful. In particular, it can't seem to find . In fact, I can't seem to find it myself -- it seems to exist in seqan/file/stream.h. However, I did a simple grep through this and other files in the archive and can't find RecordReader mentioned anywhere... I'm using version 1.3 but also took a look at the Subversion repository and can't find it either. I guess I must be doing something wrong... Any help would be appreciated; thank you! Is it related to the "beta state" message at the top of one of the Tutorial pages? Thank you! Ray From manuel.holtgrewe@fu-berlin.de Tue Nov 22 11:08:57 2011 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 <1RSnHb-0004cf-G7>; Tue, 22 Nov 2011 11:08:55 +0100 Received: from inpost2.zedat.fu-berlin.de ([130.133.4.69]) by outpost1.zedat.fu-berlin.de (Exim 4.69) with esmtp (envelope-from ) id <1RSnHb-0007qm-E7>; Tue, 22 Nov 2011 11:08:55 +0100 Received: from ecoli.imp.fu-berlin.de ([160.45.111.133]) by inpost2.zedat.fu-berlin.de (Exim 4.69) with esmtpsa (envelope-from ) id <1RSnHb-0001Ds-CB>; Tue, 22 Nov 2011 11:08:55 +0100 Message-ID: <4ECB749C.9050706@fu-berlin.de> Date: Tue, 22 Nov 2011 11:08:28 +0100 From: Manuel Holtgrewe User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:7.0.1) Gecko/20110929 Thunderbird/7.0.1 MIME-Version: 1.0 To: SeqAn Development References: <4ECB73C7.4040204@cuhk.edu.hk> In-Reply-To: <4ECB73C7.4040204@cuhk.edu.hk> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Originating-IP: 160.45.111.133 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1321956535-000067B8-DB7D3862/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Dschibuti.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=-2.0 required=5.0 tests=ALL_TRUSTED, RATWARE_GECKO_BUILD Subject: Re: [Seqan-dev] RecordReader question 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: Tue, 22 Nov 2011 10:08:57 -0000 Ray, there are no silly questions ;) Apparently, you have been confused by the SVN structure. This is a point we will address in the near future with a reorganization. You are looking for the stream.h header in the "extras" library. http://svn.mi.fu-berlin.de/seqan/trunk/seqan/extras/include/seqan/ The stream library is included in the current trunk revision. Apparently, you are using your own build/project files, i.e. not generated with the SeqAn build system. Note that you have to add both "core/include" and "extras/include" to the include path. HTH and don't hesitate to ask more questions. Manuel On 11/22/2011 11:04 AM, Raymond Wan wrote: > > Dear all, > > Sorry if this is a silly question, but I'm trying to get the > RecordReader example at: > > http://trac.mi.fu-berlin.de/seqan/browser/trunk/seqan/extras/demos/tutorial/stream/stream_read_record_fasta.cpp > > working but have been unsuccessful. In particular, it can't > seem to find. In fact, I can't seem to > find it myself -- it seems to exist in seqan/file/stream.h. > However, I did a simple grep through this and other files > in the archive and can't find RecordReader mentioned anywhere... > > I'm using version 1.3 but also took a look at the Subversion > repository and can't find it either. > > I guess I must be doing something wrong... Any help would > be appreciated; thank you! Is it related to the "beta > state" message at the top of one of the Tutorial pages? > > Thank you! > > Ray > > > > > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev From rwan@cuhk.edu.hk Wed Nov 23 07:28:43 2011 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 <1RT6K2-0002TP-2k>; Wed, 23 Nov 2011 07:28:42 +0100 Received: from cmt1.itsc.cuhk.edu.hk ([137.189.11.91]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1RT6K1-0003nu-MI>; Wed, 23 Nov 2011 07:28:42 +0100 Received: from [192.168.129.108] (unknown [210.177.253.61]) (using TLSv1 with cipher AES256-SHA (256/256 bits)) (No client certificate requested) (Authenticated sender: b126594) by cmt1.itsc.cuhk.edu.hk (Postfix) with ESMTPSA id 272C882016F for ; Wed, 23 Nov 2011 14:28:38 +0800 (HKT) Message-ID: <4ECC9295.8070105@cuhk.edu.hk> Date: Wed, 23 Nov 2011 14:28:37 +0800 From: Raymond Wan User-Agent: Mozilla/5.0 (X11; U; Linux x86_64; en-US; rv:1.9.1.16) Gecko/20111110 Icedove/3.0.11 MIME-Version: 1.0 To: SeqAn Development References: <4ECB73C7.4040204@cuhk.edu.hk> <4ECB749C.9050706@fu-berlin.de> In-Reply-To: <4ECB749C.9050706@fu-berlin.de> Content-Type: text/plain; charset=UTF-8; format=flowed Content-Transfer-Encoding: 7bit X-Originating-IP: 137.189.11.91 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1322029722-000067B8-65D82C09/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.171446, version=1.2.2 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=0.8 required=5.0 tests=RATWARE_GECKO_BUILD Subject: Re: [Seqan-dev] RecordReader question 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, 23 Nov 2011 06:28:44 -0000 Hi Manuel, Thank you for the prompt reply! On 2011-11-22 18:08, Manuel Holtgrewe wrote: > there are no silly questions ;) Apparently, you have been confused by > the SVN structure. This is a point we will address in the near future > with a reorganization. > > You are looking for the stream.h header in the "extras" library. > > http://svn.mi.fu-berlin.de/seqan/trunk/seqan/extras/include/seqan/ > > The stream library is included in the current trunk revision. Ah, I see! So, RecordReader isn't part of the current version of SeqAn? I see. I didn't realize my clicking through the documentation took me from version 1.3 to the extras. Will the extras be moved in with everything else later on? i.e., extras is for "upcoming features"? And yes, I didn't realize there was even an extras/ subdirectory... > Apparently, you are using your own build/project files, i.e. not > generated with the SeqAn build system. Note that you have to add both > "core/include" and "extras/include" to the include path. Ah, yes. I'm adding SeqAn to my CMakeLists.txt rather than adding my project to SeqAn's CMakeLists.txt. I figured if I start off with an empty file, then I have an idea of what goes inside it. SeqAn's looks great but there are a lot of cmake directives I don't quite understand. As I started off with the 1.3 release, I didn't realize there were two include paths. I guess you recommend going with the SVN trunk rather than the older 1.3 release? > HTH and don't hesitate to ask more questions. Ok! :-) and thank you for your help! Ray From manuel.holtgrewe@fu-berlin.de Wed Nov 23 09:33:12 2011 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 <1RT8GU-0006iu-DR>; Wed, 23 Nov 2011 09:33:10 +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 <1RT8GU-00017L-BR>; Wed, 23 Nov 2011 09:33:10 +0100 Received: from 91-65-212-104-dynip.superkabel.de ([91.65.212.104] helo=[192.168.0.100]) by inpost2.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtpsa (envelope-from ) id <1RT8GU-0007a4-8z>; Wed, 23 Nov 2011 09:33:10 +0100 Message-ID: <4ECCAFC6.3080003@fu-berlin.de> Date: Wed, 23 Nov 2011 09:33:10 +0100 From: Manuel Holtgrewe User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:7.0.1) Gecko/20110929 Thunderbird/7.0.1 MIME-Version: 1.0 To: SeqAn Development References: <4ECB73C7.4040204@cuhk.edu.hk> <4ECB749C.9050706@fu-berlin.de> <4ECC9295.8070105@cuhk.edu.hk> In-Reply-To: <4ECC9295.8070105@cuhk.edu.hk> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Originating-IP: 91.65.212.104 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1322037190-000067B8-37FBB883/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Algerien.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=-2.0 required=5.0 tests=ALL_TRUSTED, RATWARE_GECKO_BUILD Subject: Re: [Seqan-dev] RecordReader question 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, 23 Nov 2011 08:33:12 -0000 Ray, yes, we recommend to use the svn trunk. extras is for incubating code until it is stable enough to go into core. Furthermore, things in core should be useful to the general public and not just special cases. The following should help you to create a minimal CMakeLists.txt. It is based on Makefiles but contains the minimal setup: http://trac.mi.fu-berlin.de/seqan/wiki/HowTo/UseSeqAnInYourProjects HTH Manuel On 11/23/2011 07:28 AM, Raymond Wan wrote: > > Hi Manuel, > > Thank you for the prompt reply! > > > On 2011-11-22 18:08, Manuel Holtgrewe wrote: >> there are no silly questions ;) Apparently, you have been confused by >> the SVN structure. This is a point we will address in the near future >> with a reorganization. >> >> You are looking for the stream.h header in the "extras" library. >> >> http://svn.mi.fu-berlin.de/seqan/trunk/seqan/extras/include/seqan/ >> >> The stream library is included in the current trunk revision. > > > Ah, I see! So, RecordReader isn't part of the current > version of SeqAn? > > I see. I didn't realize my clicking through the > documentation took me from version 1.3 to the extras. > > Will the extras be moved in with everything else later on? > i.e., extras is for "upcoming features"? > > And yes, I didn't realize there was even an extras/ > subdirectory... > > >> Apparently, you are using your own build/project files, i.e. not >> generated with the SeqAn build system. Note that you have to add both >> "core/include" and "extras/include" to the include path. > > > Ah, yes. I'm adding SeqAn to my CMakeLists.txt rather than > adding my project to SeqAn's CMakeLists.txt. I figured if I > start off with an empty file, then I have an idea of what > goes inside it. SeqAn's looks great but there are a lot of > cmake directives I don't quite understand. > > As I started off with the 1.3 release, I didn't realize > there were two include paths. I guess you recommend going > with the SVN trunk rather than the older 1.3 release? > > >> HTH and don't hesitate to ask more questions. > > > Ok! :-) and thank you for your help! > > Ray > > > > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev From rwan@cuhk.edu.hk Wed Nov 23 09:40:46 2011 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 <1RT8Np-0006yg-J6>; Wed, 23 Nov 2011 09:40:45 +0100 Received: from cmt2.itsc.cuhk.edu.hk ([137.189.11.92]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1RT8No-00010k-S1>; Wed, 23 Nov 2011 09:40:45 +0100 Received: from [192.168.129.108] (unknown [210.177.253.61]) (using TLSv1 with cipher AES256-SHA (256/256 bits)) (No client certificate requested) (Authenticated sender: b126594) by cmt2.itsc.cuhk.edu.hk (Postfix) with ESMTPSA id A3CC6E89065 for ; Wed, 23 Nov 2011 16:40:40 +0800 (HKT) Message-ID: <4ECCB188.80706@cuhk.edu.hk> Date: Wed, 23 Nov 2011 16:40:40 +0800 From: Raymond Wan User-Agent: Mozilla/5.0 (X11; U; Linux x86_64; en-US; rv:1.9.1.16) Gecko/20111110 Icedove/3.0.11 MIME-Version: 1.0 To: SeqAn Development References: <4ECB73C7.4040204@cuhk.edu.hk> <4ECB749C.9050706@fu-berlin.de> <4ECC9295.8070105@cuhk.edu.hk> In-Reply-To: <4ECC9295.8070105@cuhk.edu.hk> Content-Type: text/plain; charset=UTF-8; format=flowed Content-Transfer-Encoding: 7bit X-Originating-IP: 137.189.11.92 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1322037645-000067B8-CEDABEBB/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.198932, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Burundi.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=0.8 required=5.0 tests=RATWARE_GECKO_BUILD Subject: Re: [Seqan-dev] RecordReader question 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, 23 Nov 2011 08:40:46 -0000 Hi Manuel, On 2011-11-23 14:28, Raymond Wan wrote: >> Apparently, you are using your own build/project files, i.e. not >> generated with the SeqAn build system. Note that you have to add both >> "core/include" and "extras/include" to the include path. > Ah, yes. I'm adding SeqAn to my CMakeLists.txt rather than adding my > project to SeqAn's CMakeLists.txt. I figured if I start off with an > empty file, then I have an idea of what goes inside it. SeqAn's looks > great but there are a lot of cmake directives I don't quite understand. I'm starting to have doubts about what I'm doing is a good idea... Perhaps you can tell me what I'm doing wrong? If I'm not mistaken, SeqAn is a header-only library (like most of Boost). And compiling is only needed if you want to look at the tutorials? The 1.3 Release instructions says that I just have to move the include/ directory to the right place. So, I created the subdirectories: ~/common/include/seqan-core ~/common/include/seqan-extras Inside seqan-core, I have a symlink: seqan -> ../seqan/core/include/seqan Likewise for seqan-extras. In CMakeLists.txt, I did this: INCLUDE_DIRECTORIES (~/common/include/seqan-core) INCLUDE_DIRECTORIES (~/common/include/seqan-extras) ...I think this should work? In my source, I did: #include #include When I compile, I get this error: In file included from /home/rwan/common/include/seqan-core/seqan/platform.h:43, from /home/rwan/common/include/seqan-core/seqan/basic.h:39, ... /home/rwan/common/include/seqan-core/seqan/platform/platform_gcc.h:82:56: error: seqan/platform/platform_generated_forwards.h: No such file or directory /home/rwan/common/include/seqan-core/seqan/platform/platform_gcc.h:85:2: error: #error To use the SeqAn library you first have to execute 'make forwards' in the root directory ... So, it found basic.h, platform.h, ... fine, but not platform_generated_forwards.h . The error says I need to do a 'make forwards' but: 1) I don't know what is the root directory; or, at least one with an obvious makefile. 2) I could perform an out-of-source build and create a build/ directory and do "cmake | make" but that didn't copy the header files over -- moving the symlinks to this build/ directory doesn't seem to work. I think I'm close :-) but I'm still stuck. My only remaining idea is to do an in-source build -- such that the stuff that is created with "make" is in the same place where the .h files are. Is that what I need to do? Thank you and if I'm confusing myself and should just follow the instructions and work from SeqAn's CMakeLists.txt, please tell me. :-) Ray PS: This is the SVN release. I'm not using 1.3 anymore. ;-) From rwan@cuhk.edu.hk Wed Nov 23 09:54:37 2011 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 <1RT8bE-0007aW-1s>; Wed, 23 Nov 2011 09:54:36 +0100 Received: from photon.itsc.cuhk.edu.hk ([137.189.11.93]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1RT8bD-0002fb-LE>; Wed, 23 Nov 2011 09:54:36 +0100 Received: from [192.168.129.108] (unknown [210.177.253.61]) (using TLSv1 with cipher AES256-SHA (256/256 bits)) (No client certificate requested) (Authenticated sender: b126594) by photon.itsc.cuhk.edu.hk (Postfix) with ESMTPSA id 78EEF390363 for ; Wed, 23 Nov 2011 16:54:31 +0800 (HKT) Message-ID: <4ECCB4C7.2070805@cuhk.edu.hk> Date: Wed, 23 Nov 2011 16:54:31 +0800 From: Raymond Wan User-Agent: Mozilla/5.0 (X11; U; Linux x86_64; en-US; rv:1.9.1.16) Gecko/20111110 Icedove/3.0.11 MIME-Version: 1.0 To: SeqAn Development References: <4ECB73C7.4040204@cuhk.edu.hk> <4ECB749C.9050706@fu-berlin.de> <4ECC9295.8070105@cuhk.edu.hk> <4ECCAFC6.3080003@fu-berlin.de> In-Reply-To: <4ECCAFC6.3080003@fu-berlin.de> Content-Type: text/plain; charset=UTF-8; format=flowed Content-Transfer-Encoding: 7bit X-Originating-IP: 137.189.11.93 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1322038476-000067B8-F29CF995/0-0/0-0 X-Bogosity: Unsure, tests=bogofilter, spamicity=0.484278, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Botsuana.ZEDAT.FU-Berlin.DE X-Spam-Level: xx X-Spam-Status: No, score=2.3 required=5.0 tests=FU_BOGO_UNSURE, RATWARE_GECKO_BUILD Subject: Re: [Seqan-dev] RecordReader question 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, 23 Nov 2011 08:54:37 -0000 Hi Manuel, Sorry, but I was busy typing my previous message and didn't notice his message of your's come in. It seems to answer my questions...I'm going to give a try now. Thank you! Read my mind...or just predicted what would be the next thing I would stumble on. ;-) Ray On 2011-11-23 16:33, Manuel Holtgrewe wrote: > yes, we recommend to use the svn trunk. extras is for incubating code > until it is stable enough to go into core. Furthermore, things in core > should be useful to the general public and not just special cases. > > > The following should help you to create a minimal CMakeLists.txt. It is > based on Makefiles but contains the minimal setup: > > http://trac.mi.fu-berlin.de/seqan/wiki/HowTo/UseSeqAnInYourProjects From manuel.holtgrewe@fu-berlin.de Wed Nov 23 14:53:44 2011 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 <1RTDGi-0001P1-5F>; Wed, 23 Nov 2011 14:53:44 +0100 Received: from inpost2.zedat.fu-berlin.de ([130.133.4.69]) by outpost1.zedat.fu-berlin.de (Exim 4.69) with esmtp (envelope-from ) id <1RTDGi-0008SY-2p>; Wed, 23 Nov 2011 14:53:44 +0100 Received: from ecoli.imp.fu-berlin.de ([160.45.111.133]) by inpost2.zedat.fu-berlin.de (Exim 4.69) with esmtpsa (envelope-from ) id <1RTDGi-0006Y2-0q>; Wed, 23 Nov 2011 14:53:44 +0100 Message-ID: <4ECCFACC.20504@fu-berlin.de> Date: Wed, 23 Nov 2011 14:53:16 +0100 From: Manuel Holtgrewe User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:7.0.1) Gecko/20110929 Thunderbird/7.0.1 MIME-Version: 1.0 To: SeqAn Development Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Originating-IP: 160.45.111.133 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1322056424-000067B8-7543DF65/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.2.2 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=-2.0 required=5.0 tests=ALL_TRUSTED, RATWARE_GECKO_BUILD Subject: [Seqan-dev] Scheduled Maintenance of trac.mi.fu-berlin.de/seqan 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, 23 Nov 2011 13:53:44 -0000 Dear all, this Friday (2011-11-25), we will have a scheduled maintenance and downtime of our Trac instance. Bests, Manuel