From bjpope@unimelb.edu.au Sun Jul 10 08:35:34 2016 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtps (TLSv1.2:DHE-RSA-AES256-GCM-SHA384:256) (envelope-from ) id <1bM8Kz-000ZIE-7h>; Sun, 10 Jul 2016 08:35:33 +0200 Received: from mail-sy3aus01on0050.outbound.protection.outlook.com ([104.47.117.50] helo=AUS01-SY3-obe.outbound.protection.outlook.com) by relay1.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtps (TLSv1.2:AES256-SHA256:256) (envelope-from ) id <1bM8Ky-002TMe-5u>; Sun, 10 Jul 2016 08:35:33 +0200 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=unimelb.edu.au; s=selector1; h=From:Date:Subject:Message-ID:Content-Type:MIME-Version; bh=aVxFX9Vsedub5Wh28knKhqMKHOFaIqtLmKftHwqSdYU=; b=CCVN7K4PkL7ejHoFPYaVwGN9zZYjglQoWv4T19fHBtztprZvkWahZE4aGmO0PZg6iPy2XKGe77YWiSyr4ls2RCgW0u+N+6PnbBTjUUhE9wvltjzz6kRxukUfUQwcdAoWax+lK10usVZ7MKBs1Q6zjq7W994Jt/ryFZ45zm1j84I= Received: from MEXPR01CA0047.ausprd01.prod.outlook.com (10.164.161.14) by ME1PR01MB0417.ausprd01.prod.outlook.com (10.162.67.149) with Microsoft SMTP Server (TLS) id 15.1.534.14; Sun, 10 Jul 2016 06:35:24 +0000 Received: from DB3FFO11FD001.protection.gbl (2a01:111:f400:7e04::172) by MEXPR01CA0047.outlook.office365.com (2a01:111:e400:5a6a::14) with Microsoft SMTP Server (TLS) id 15.1.534.14 via Frontend Transport; Sun, 10 Jul 2016 06:35:24 +0000 Authentication-Results: spf=pass (sender IP is 128.250.6.61) smtp.mailfrom=unimelb.edu.au; lists.fu-berlin.de; dkim=none (message not signed) header.d=none;lists.fu-berlin.de; dmarc=pass action=none header.from=unimelb.edu.au; Received-SPF: Pass (protection.outlook.com: domain of unimelb.edu.au designates 128.250.6.61 as permitted sender) receiver=protection.outlook.com; client-ip=128.250.6.61; helo=000s-ex-tmg-np2.unimelb.edu.au; Received: from 000s-ex-tmg-np2.unimelb.edu.au (128.250.6.61) by DB3FFO11FD001.mail.protection.outlook.com (10.47.216.90) with Microsoft SMTP Server (TLS) id 15.1.523.9 via Frontend Transport; Sun, 10 Jul 2016 06:35:22 +0000 Received: from 000s-ex-hub-qs1.unimelb.edu.au (172.22.46.20) by 000s-ex-tmg-np2.unimelb.edu.au (172.22.174.5) with Microsoft SMTP Server (TLS) id 14.3.301.0; Sun, 10 Jul 2016 16:34:49 +1000 Received: from 000s-ex-mbx-qs3.unimelb.edu.au ([fe80::7927:6f94:cdb:98f3]) by 000s-ex-hub-qs1.unimelb.edu.au ([fe80::3cef:7508:b0e0:4f5d%18]) with mapi id 14.03.0301.000; Sun, 10 Jul 2016 16:35:17 +1000 From: Bernard James Pope To: "seqan-dev@lists.fu-berlin.de" Thread-Topic: ArgParseArgument list allowing zero or more items? 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Ip=[128.250.6.61]; Helo=[000s-ex-tmg-np2.unimelb.edu.au] X-MS-Exchange-CrossTenant-FromEntityHeader: HybridOnPrem X-MS-Exchange-Transport-CrossTenantHeadersStamped: ME1PR01MB0417 X-Originating-IP: 104.47.117.50 X-Original-X-Originating-IP: [172.20.127.15] X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1468132533-0000049F-01E715AE/0/0 X-Bogosity: Unsure, tests=bogofilter, spamicity=0.500116, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=1.4 required=5.0 tests=DKIM_SIGNED,DKIM_VALID, DKIM_VALID_AU,FU_BOGO_UNSURE,RCVD_IN_DNSWL_NONE,SPF_HELO_PASS,SPF_PASS X-Spam-Checker-Version: SpamAssassin 3.4.1 on Kiribati.ZEDAT.FU-Berlin.DE X-Spam-Level: x Subject: [Seqan-dev] ArgParseArgument list allowing zero or more items? X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.16 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Sun, 10 Jul 2016 06:35:34 -0000 Hi SEQAN devs, I'm writing a program which accepts zero or more FASTA files on the command= line, as positional arguments. If zero files are specified, then it will default to reading from standard = input. I want to write a Seqan argument parser to capture this behaviour. However,= I seem stuck with a solution that requires at least one file to be specifi= ed. Here's a sketch of what I have: ArgumentParser parser(PROGRAM_NAME); addOption(parser, ArgParseOption("f", "foo", "Silly example", ArgParseAr= gument::INTEGER, "INT")); addArgument(parser, ArgParseArgument(ArgParseArgument::STRING, "FASTA_FI= LE", true)); ArgumentParser::ParseResult res =3D parse(parser, argc, argv); Notice that isListArgument is set to true. However, when I run my program, and specify zero positional arguments (but = some other option arguments), e.g. $ myprogram -foo 0 I get the error: Not enough arguments were provided. Is there a way to achieve what I want to do? I thought I might be able to default the ArgParseArgument to be an empty ve= ctor somehow, but couldn't get that to work. If anyone has used the Python ArgumentParser before, the behaviour I want t= o emulate is the ability to specify nargs=3D'*' Cheers, Bernie= From hannes.hauswedell@fu-berlin.de Thu Jul 14 17:40:22 2016 Received: from outpost1.zedat.fu-berlin.de ([130.133.4.66]) by list1.zedat.fu-berlin.de (Exim 4.85) with esmtps (TLSv1.2:DHE-RSA-AES256-GCM-SHA384:256) (envelope-from ) id <1bNikQ-000yl4-9Q>; Thu, 14 Jul 2016 17:40:22 +0200 Received: from inpost2.zedat.fu-berlin.de ([130.133.4.69]) by outpost.zedat.fu-berlin.de (Exim 4.85) with esmtps (TLSv1.2:DHE-RSA-AES256-GCM-SHA384:256) (envelope-from ) id <1bNikQ-003tdu-5x>; Thu, 14 Jul 2016 17:40:22 +0200 Received: from celegans.imp.fu-berlin.de ([160.45.111.134]) by inpost2.zedat.fu-berlin.de (Exim 4.85) with esmtpsa (TLSv1:DHE-RSA-AES256-SHA:256) (envelope-from ) id <1bNikP-00098J-Sm>; Thu, 14 Jul 2016 17:40:22 +0200 From: Hannes Hauswedell To: seqan-dev@lists.fu-berlin.de, seqan-team@lists.fu-berlin.de Date: Thu, 14 Jul 2016 17:40:20 +0200 Message-ID: <1908599.vRoPXqX8r3@celegans.imp.fu-berlin.de> Organization: MPI MolGen / FU-Berlin MIME-Version: 1.0 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" X-Originating-IP: 160.45.111.134 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1468510822-0000049F-82442E6B/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=-51.3 required=5.0 tests=ALL_TRUSTED, RP_MATCHES_RCVD, T_FILL_THIS_FORM_SHORT X-Spam-Checker-Version: SpamAssassin 3.4.1 on Kiribati.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: [Seqan-dev] SeqAn 2.2 released X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.16 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, 14 Jul 2016 15:40:22 -0000 Dear users and programmers,=20 We are pleased to announce the release of version 2.2 of the SeqAn libr= ary and=20 updated versions of the official SeqAn-based applications. New features= =20 include the preliminary addition of a bi-directional FM-Index and a new= =20 interface for performing multiple sequence alignments at the same time.= The=20 latter uses SIMD [1] features of modern processors to perform up to 16=20= alignments in parallel *per cpu-core* (in addition to possible applicat= ion=20 level multi-threading). Important "under the hood" changes include the=20= replacement of SeqAn's custom threading framework with C++11's thread l= ibrary.=20 This fixes some rare, but long-standing bugs in BAM I/O and improves=20= performance slightly. There are also major infrastructural changes, including support for the= Intel=20 Compiler on all platforms and also experimental support for Clang/C2 on= =20 Windows [2]. For the official applications many fixes and improvements = to the=20 build system have made all new and optimized binaries possible that wor= k on=20 even more platforms. All publicly documented interfaces are preserved and no supported platf= orms=20 where dropped. It is now our policy that this shall not happen in the 2= .x=20 cycle anymore at all so you can trust that your applications work with = the=20 next releases. Do note, however, that we dropped some interfaces and su= pported=20 platforms between 2.0 and 2.1. **Further links** Full Changelog: https://github.com/seqan/seqan/blob/master/CHANGELOG.rs= t=20 Downloads: http://packages.seqan.de/ New Homepage: https://www.seqan.de [1] https://en.wikipedia.org/wiki/SIMD [2] https://blogs.msdn.microsoft.com/vcblog/2015/12/04/clang-with-micro= soft-codegen-in-vs-2015-update-1/ Best regards, --=20 Hannes Hauswedell PhD candidate Max Planck Institute for Molecular Genetics / Freie Universit=C3=A4t Be= rlin address Institut f=C3=BCr Informatik Takustra=C3=9Fe 9 Room 019 14195 Berlin telephone +49 (0)30 838-75241 fax +49 (0)30 838-75218 e-mail hannes.hauswedell@[molgen.mpg.de|fu-berlin.de] From rene.maerker@fu-berlin.de Thu Jul 28 12:00:35 2016 Received: from outpost9.zedat.fu-berlin.de ([130.133.4.95]) by list1.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtps (TLSv1.2:DHE-RSA-AES256-GCM-SHA384:256) (envelope-from ) id <1bSi7G-001yge-6t>; Thu, 28 Jul 2016 12:00:34 +0200 Received: from relay2.zedat.fu-berlin.de ([130.133.4.80]) by outpost.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtps (TLSv1.2:DHE-RSA-AES256-GCM-SHA384:256) (envelope-from ) id <1bSi7G-002ivw-3N>; Thu, 28 Jul 2016 12:00:34 +0200 Received: from cas3.campus.fu-berlin.de ([130.133.170.203]) by relay2.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtps (TLSv1:AES256-SHA:256) (envelope-from ) id <1bSi7F-003NxK-SR>; Thu, 28 Jul 2016 12:00:34 +0200 Received: from EX03B.campus.fu-berlin.de ([130.133.170.135]) by CAS3.campus.fu-berlin.de ([130.133.170.203]) with mapi id 14.03.0301.000; Thu, 28 Jul 2016 12:00:33 +0200 From: =?utf-8?B?UmFobiwgUmVuw6k=?= To: SeqAn Development Thread-Topic: [Seqan-dev] ArgParseArgument list allowing zero or more items? 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(envelope-from ) id <1bSiSZ-000I0o-9q>; Thu, 28 Jul 2016 12:22:35 +0200 Received: by mail-oi0-f48.google.com with SMTP id l65so56503582oib.1 for ; Thu, 28 Jul 2016 03:22:34 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20120113; h=mime-version:subject:from:in-reply-to:date :content-transfer-encoding:message-id:references:to; bh=x8/U40nF0JBY1oRd4F98uQYnh0mYoY2b1T/sXV8sW74=; b=pMFcuFKs0rtvJlL/h2+4nilJPPlaA3ATfN8vJg+fnBEQwq19nGrj33bDz9hbJxrhNO AsgzkbcZ8F9TNr/Wzb3djIUwplIfxdOym1HbkxZffU5o0EyRhTWwENhBBv8HhnL/NFYD C3L0f52nJFTo8TrDIwGsLGd0SYNO1L9kkSvsBMkV+Nh/GMAYDXAMpKGImeLfg6l7jEkh C93/Y8W6TBhCKDY00d77pSXBBozLoj3/x37joCvCGOlgc+p70WuO/O5l0oGG22nuHV7Q du8L7HUmBDxTcZuyZeuvKE2bAYj48PbgDMtM0RetHusKfwtxBnurv09tL2//JEhVF9w2 4U7A== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20130820; h=x-gm-message-state:mime-version:subject:from:in-reply-to:date :content-transfer-encoding:message-id:references:to; 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03:22:30 -0700 Content-Transfer-Encoding: quoted-printable Message-Id: <4A2703E2-46B5-497D-8884-1FF6A65AEE07@gmail.com> References: To: SeqAn Development X-Mailer: Apple Mail (2.3124) X-Originating-IP: 209.85.218.48 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1469701355-0000049F-E801477C/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.070513, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=-0.6 required=5.0 tests=DKIM_SIGNED,DKIM_VALID, DKIM_VALID_AU,FREEMAIL_ENVFROM_END_DIGIT,FREEMAIL_FROM,RCVD_IN_DNSWL_LOW, RCVD_IN_MSPIKE_H2,SPF_PASS X-Spam-Checker-Version: SpamAssassin 3.4.1 on Niue.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] ArgParseArgument list allowing zero or more items? X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.16 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, 28 Jul 2016 10:22:36 -0000 I think I=E2=80=99m confused the present way you have it would have the = an option and an argument.=20 my program -foo 0 somefasta.fasta In this case, what is the point of foo? Since you put the fasta file as an argument and not an option, it must = be specified. I think what you want is to add the fasta file as an = option then use the getOptionValue method to see if it has been used.=20 Jordan > On Jul 9, 2016, at 11:35 PM, Bernard James Pope = wrote: >=20 > Hi SEQAN devs, >=20 > I'm writing a program which accepts zero or more FASTA files on the = command line, as positional arguments. >=20 > If zero files are specified, then it will default to reading from = standard input. >=20 > I want to write a Seqan argument parser to capture this behaviour. = However, I seem stuck with a solution that requires at least one file to = be specified. >=20 > Here's a sketch of what I have: >=20 > ArgumentParser parser(PROGRAM_NAME); > addOption(parser, ArgParseOption("f", "foo", "Silly example", = ArgParseArgument::INTEGER, "INT")); >=20 > addArgument(parser, ArgParseArgument(ArgParseArgument::STRING, = "FASTA_FILE", true)); >=20 > ArgumentParser::ParseResult res =3D parse(parser, argc, argv); >=20 > Notice that isListArgument is set to true. >=20 > However, when I run my program, and specify zero positional arguments = (but some other option arguments), e.g. >=20 > $ myprogram -foo 0 >=20 > I get the error: >=20 > Not enough arguments were provided. >=20 > Is there a way to achieve what I want to do? >=20 > I thought I might be able to default the ArgParseArgument to be an = empty vector somehow, but couldn't get that to work. >=20 > If anyone has used the Python ArgumentParser before, the behaviour I = want to emulate is the ability to specify nargs=3D'*' >=20 > Cheers, > Bernie > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev From jwillis0720@gmail.com Thu Jul 28 12:34:08 2016 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtps (TLSv1.2:DHE-RSA-AES256-GCM-SHA384:256) (envelope-from ) id <1bSidj-002IRE-KG>; Thu, 28 Jul 2016 12:34:07 +0200 Received: from mail-oi0-f44.google.com ([209.85.218.44]) by relay1.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtps (TLSv1.2:AES128-GCM-SHA256:128) (envelope-from ) id <1bSidj-000Lml-7g>; Thu, 28 Jul 2016 12:34:07 +0200 Received: by mail-oi0-f44.google.com with SMTP id w18so56857831oiw.3 for ; Thu, 28 Jul 2016 03:34:06 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20120113; h=from:message-id:mime-version:subject:date:references:to:in-reply-to; bh=hliWQ4Wq/Qa0aDeaK+nuJt5YRCKQpGBLsKw/HAsiGEw=; b=SU4+nmsEIEpHWGz7PcRUQ/xc3TSslWWkkQbi8x/1R5j9a/76sPTBlcIIAvIx5k6fw1 wnYp9CddYvkaLIgMsXjpX3pn+Zd3L5wzk/ZbeTsnDzf0x/rhgttW8fkc7q0fw8Qkbi0f A0AtMWcl+REvtmwFqZSRhGxxKC9htM7d02H9ck7Vohf73rWZm1dAfJc2UXFDRaKywiDF tD/ynXlq8nIt3tLoeX38ePeeFIcEona3YZupOD+t8lFF16MvAcyeVTkLDVDdUKxIFgaR IoY15XBqth5G0RZUWnHHrzxxwJ9bufwEGCw8fPRE6/xTZ1c143RRdUNbQG8LvhaVuul/ n4RA== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20130820; h=x-gm-message-state:from:message-id:mime-version:subject:date :references:to:in-reply-to; bh=hliWQ4Wq/Qa0aDeaK+nuJt5YRCKQpGBLsKw/HAsiGEw=; b=GwV6NTGAQXMSTocOJ9PRxfCr1/PJzlx8+qcMqTaQxdlU8r3S396nw8N/LFt8oTT1MT E+Dqgo9RkKCHSnnd4BGA6r8ko4X1CukPh1yVu/Aax5PeNEc4iBSp5kFn1HToOxHNNPfF YTtvnyTRIgOaFor5d93F7pJ0lTCzTRnEJP8Pcu08iZkKooeOX5CBmtB1v9lFdmqvDPpU UPFlco3bxKHkJ6bGsTxD8CVws9eVCl4AS5a1TdGzvzQV3pGPlLCtvBtjV8sg9tZKsnUl kftOhCjCJ0csSTTP+yG9s6N1ox+plj7EgNBxldDMnNsvreT31wTkQjcPUWVxo+lAM4Ex BpdQ== X-Gm-Message-State: AEkoouss2KPY9fO8p/MPrBCZR7UK115j1xna/Wn3XfJjLEj00TcEp3RLoSjGecnhog+VVA== X-Received: by 10.157.46.97 with SMTP id c30mr19399919otd.14.1469702044585; Thu, 28 Jul 2016 03:34:04 -0700 (PDT) Received: from hal10k.attlocal.net ([2602:30a:2e73:9790:51:559d:8f8b:98a5]) by smtp.gmail.com with ESMTPSA id g10sm4346520otb.35.2016.07.28.03.34.03 for (version=TLS1 cipher=ECDHE-RSA-AES128-SHA bits=128/128); Thu, 28 Jul 2016 03:34:04 -0700 (PDT) From: Jordan Willis Content-Type: multipart/alternative; boundary="Apple-Mail=_EAF51924-246F-4B91-9D56-A7014840E685" Message-Id: <29E69648-0285-4B38-9452-663F8505DB05@gmail.com> Mime-Version: 1.0 (Mac OS X Mail 9.3 \(3124\)) Date: Thu, 28 Jul 2016 03:34:02 -0700 References: To: SeqAn Development In-Reply-To: X-Mailer: Apple Mail (2.3124) X-Originating-IP: 209.85.218.44 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1469702047-0000049F-9690A6FB/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.087839, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=0.5 required=5.0 tests=DKIM_SIGNED,DKIM_VALID, DKIM_VALID_AU,FREEMAIL_ENVFROM_END_DIGIT,FREEMAIL_FROM,FREEMAIL_REPLY, HTML_MESSAGE,RCVD_IN_DNSWL_LOW,RCVD_IN_MSPIKE_H2,SPF_PASS X-Spam-Checker-Version: SpamAssassin 3.4.1 on Vanuatu.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] Annotation and spliced site X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.16 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, 28 Jul 2016 10:34:08 -0000 --Apple-Mail=_EAF51924-246F-4B91-9D56-A7014840E685 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=utf-8 Hi Rene, github issues seem to one place, but have you guys thought about = deploying your own seqan q & a for end users? It=E2=80=99s like stack overflow but just for seqan=20 https://github.com/ialbert/biostar-central = > On Jul 28, 2016, at 3:01 AM, Rahn, Ren=C3=A9 = wrote: >=20 > Hi Yue,=20 >=20 > thank you very much for writing us and sorry for keeping you on the = loop for so long.=20 > I'd like you to raise such questions on the issue site on our github = page: https://github.com/seqan/seqan/issues = . > The mailing list is not-so-up-to-date anymore, and we will probably = use this mailing list merely as a news feeder in the future to inform = you about new releases or training courses. >=20 > Thank you very much for you understanding. >=20 > Kind regards, >=20 > Ren=C3=A9 >> On 14 Jun 2016, at 06:14, Yue Gan > wrote: >>=20 >> Hi all, >>=20 >> I am trying to use the annotation part of Seqan to solve a question, = but I am a little bit confused. >>=20 >> What I want to do is to >> 1. Read in an annotation file (the format can be GFF, GTF, or BED) >> 2. Giving two positions (q1, q2) in the genome, decide if (q1, q2) is = a known junction. >>=20 >> My Solution: >> 1. use GffFile in to load the annotation file(GFF, GTF) into a = FragmentStore<> >> 2. extract the exons and create a junction Interval tree using the = FragmentStore<> >> 3. using interval`s 'findIntervals' function giving q1 and q2 to find = if there is an interval(junction) exists. >>=20 >> My Question: >> 1. Is BED better then GFF and GTF in this situation? >> 2. If BED is better, could anybody give me some examples what seqan = data structure I should use to store and do the search? Some pseudocode = with seqan data structure and function could be better.... >> 3. If GFF and GTF are better, is my solution correct and efficient? = Is there any better way to solve my question? Is there anything I need = to pay attention to? >>=20 >> Thank you very much! >>=20 >> Yue Gan >> _______________________________________________ >> seqan-dev mailing list >> seqan-dev@lists.fu-berlin.de >> https://lists.fu-berlin.de/listinfo/seqan-dev >=20 > --- >=20 > Ren=C3=A9 Rahn > Ph.D. Student (de.NBI - CIBI) > -------------------------------- > Tel: (+49) 30 838 75137 > Mail: rene.rahn@fu-berlin.de > -------------------------------- > Institute of Computer Science > Algorithmic Bioinformatics (ABI) > -------------------------------- > Freie Universit=C3=A4t Berlin > Takustra=C3=9Fe 9 > 14195 Berlin > -------------------------------- >=20 > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev --Apple-Mail=_EAF51924-246F-4B91-9D56-A7014840E685 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=utf-8 Hi Rene,

github issues seem to one place, but have you guys thought = about deploying your own seqan q & a for end users?

It=E2=80=99s like stack = overflow but just for seqan 



On = Jul 28, 2016, at 3:01 AM, Rahn, Ren=C3=A9 <rene.maerker@fu-berlin.de> wrote:

Hi Yue, 

thank you very much for writing us and sorry for keeping = you on the loop for so long. 
I'd like you to raise such questions on the issue site = on our github page: https://github.com/seqan/seqan/issues.
The mailing list is not-so-up-to-date anymore, and we = will probably use this mailing list merely as a news feeder in the = future to inform you about new releases or training courses.

Thank you very much for you understanding.

Kind regards,

Ren=C3=A9
On 14 Jun 2016, at 06:14, Yue Gan <gany.fml@gmail.com> = wrote:

Hi all,

I am trying to use the annotation part of Seqan to solve = a question, but I am a little bit confused.

What I want to do is to
1. Read in an annotation file (the format can be GFF, = GTF, or BED)
2. Giving two positions (q1, q2) in the genome, decide = if (q1, q2) is a known junction.

My Solution:
1. use GffFile in to load the annotation file(GFF, GTF) = into a FragmentStore<>
2. extract the exons and create a junction Interval tree = using the FragmentStore<>
3. using interval`s 'findIntervals' function giving q1 = and q2 to find if there is an interval(junction) exists.

My Question:
1. Is BED better then GFF and GTF in this = situation?
2. If BED is better, could anybody give me some examples = what seqan data structure I should use to store and do the search? = Some pseudocode with seqan data structure and function could = be better....
3. If GFF and GTF are better, is my solution correct and = efficient? Is there any better way to solve my question? Is there = anything I need to pay attention to?

Thank you very much!

Yue Gan
_______________________________________________
seqan-dev mailing list
seqan-dev@lists.fu-berlin.de
https://lists.fu-berlin.de/listinfo/seqan-dev

---

Ren=C3=A9 Rahn
Ph.D. Student (de.NBI - CIBI)
--------------------------------
Tel:  (+49) = 30 838 75137
--------------------------------
Institute of Computer Science
Algorithmic Bioinformatics (ABI)
--------------------------------
Freie Universit=C3=A4t Berlin
Takustra=C3=9Fe 9
14195 Berlin
--------------------------------

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

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