From sebastien.moretti at unil.ch Fri Feb 1 04:15:55 2013 From: sebastien.moretti at unil.ch (=?ISO-8859-1?Q?Moretti_S=E9bastien?=) Date: Fri, 01 Feb 2013 10:15:55 +0100 Subject: [EMBOSS] emma and clustalw2 In-Reply-To: <510A9DD1.4020303@ebi.ac.uk> References: <510A95FB.3040103@unil.ch> <510A9DD1.4020303@ebi.ac.uk> Message-ID: <510B87CB.9040400@unil.ch> Hi Mahmut, Thanks it works nicely this way. So, move back to external: "clustalw" and use EMBOSS_CLUSTALW variable. > Hi Sebastien, > > It looks if I set EMBOSS_CLUSTALW environment variable to point to > clustalw2 executable, as in the following example, i don't need to > modify the emma.acd file. > > export EMBOSS_CLUSTALW=~/esbin/clustalw-2.1/bin/clustalw2 > > Regards, > Mahmut > >> I try to use emma (v 6.5.7.0) with clustalw2 (v 2.1) on Linux x86_64. >> My environment contains both clustalw and clustalw2, that's why >> clustalw2 binary is called clustalw2. >> Accordingly I have changed this line in the emma.acd file (before >> compilation): >> external: "clustalw2" >> instead of >> external: "clustalw" >> >> >> When I try to run emma, I get this error message: >> >> Multiple sequence alignment (ClustalW wrapper) >> Warning: Cannot find 'clustalw', no ACD external definition found >> Error: Failed to open filename '00011120B' >> Problem writing out EMBOSS alignment file >> Error: File 'msf::00011120B' remove failed, error:2 'No such file or >> directory' -- S?bastien Moretti SIB Vital-IT EMBnet, Quartier Sorge - Genopode CH-1015 Lausanne, Switzerland Tel.: +41 (21) 692 4079/4221 http://www.vital-it.ch/ http://myhits.vital-it.ch/ From daniel.rozenbaum at USPTO.GOV Wed Feb 6 10:50:00 2013 From: daniel.rozenbaum at USPTO.GOV (Rozenbaum, Daniel (Biocceleration Inc)) Date: Wed, 6 Feb 2013 10:50:00 -0500 Subject: [EMBOSS] Working with Geneseq databases Message-ID: Dear all, Does anyone have experience getting EMBOSS to work with the Geneseq database distributed by Thomson Reuters ( http://thomsonreuters.com/products_services/science/science_products/a-z/geneseq/ ) ? This database comes in "EMBL-like" format that uses some line codes that are not defined in EMBL format proper, which in our experiments has caused problems when, for example, trying to index these databases as EMBL-formatted. -- Daniel Rozenbaum Biocceleration, Inc. OCIO/Office of Application Engineering and Development/Patent System Division 600 Dulany St., Alexandria, VA 22314 From isabelle.wells at roche.com Thu Feb 7 05:14:08 2013 From: isabelle.wells at roche.com (Wells, Isabelle) Date: Thu, 7 Feb 2013 11:14:08 +0100 Subject: [EMBOSS] Working with Geneseq databases In-Reply-To: References: Message-ID: <2489C38FDAFBFD41B59E3156253FFA6E0286DDDD55@rkamsem703.emea.roche.com> Hi Daniel, We index the geneseq databases in the EMBL format. The problem with Geneseq format is that each entry has several lines starting with "SQ ". Therefore in order to make this work you just need to write a program which only prints the first line starting with "SQ " in each entry and skips the following SQ lines. Hope this helps! Best regards, Isabelle Wells F. Hoffmann-La Roche Ltd? -----Original Message----- From: emboss-bounces at lists.open-bio.org [mailto:emboss-bounces at lists.open-bio.org] On Behalf Of Rozenbaum, Daniel (Biocceleration Inc) Sent: Wednesday, 6. February 2013 16:50 To: emboss at lists.open-bio.org Subject: [EMBOSS] Working with Geneseq databases Dear all, Does anyone have experience getting EMBOSS to work with the Geneseq database distributed by Thomson Reuters ( http://thomsonreuters.com/products_services/science/science_products/a-z/geneseq/ ) ? This database comes in "EMBL-like" format that uses some line codes that are not defined in EMBL format proper, which in our experiments has caused problems when, for example, trying to index these databases as EMBL-formatted. -- Daniel Rozenbaum Biocceleration, Inc. OCIO/Office of Application Engineering and Development/Patent System Division 600 Dulany St., Alexandria, VA 22314 _______________________________________________ EMBOSS mailing list EMBOSS at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss From daniel.rozenbaum at USPTO.GOV Thu Feb 7 09:27:57 2013 From: daniel.rozenbaum at USPTO.GOV (Rozenbaum, Daniel (Biocceleration Inc)) Date: Thu, 7 Feb 2013 09:27:57 -0500 Subject: [EMBOSS] Working with Geneseq databases In-Reply-To: <2489C38FDAFBFD41B59E3156253FFA6E0286DDDD55@rkamsem703.emea.roche.com> References: , <2489C38FDAFBFD41B59E3156253FFA6E0286DDDD55@rkamsem703.emea.roche.com> Message-ID: Hi Isabelle, Thanks a lot for your feedback. I might be doing something wrong, but even after I remove the extra SQ lines, dbiflat still fails with something like EMBOSS An error in embdbi.c at line 1569: Error in embDbiSortWriteFields, expected entry not found, last was 'BAD10932' Have you seen anything like this by any chance? Looking at the ".acnum_sort" dbiflat creates, it appears that dbiflat misinterprets some of the lines with non-standard line type codes like "PA", and appears to treat the strings in those lines as accession numbers. Not sure if my interpretation of what I'm seeing is correct, and whether this is what's causing the error I mentioned above. What I did try was to simply add the "CC" line type code at the beginning of any line whose line type code is not in EMBL standard. This seems to have done the trick, but I'm wondering if it's the best way to go. If it matters, we're using EMBOSS 6.4.0 . Many thanks, Daniel ________________________________________ From: emboss-bounces at lists.open-bio.org [emboss-bounces at lists.open-bio.org] On Behalf Of Wells, Isabelle [isabelle.wells at roche.com] Sent: Thursday, February 07, 2013 5:14 AM To: emboss at lists.open-bio.org Subject: Re: [EMBOSS] Working with Geneseq databases Hi Daniel, We index the geneseq databases in the EMBL format. The problem with Geneseq format is that each entry has several lines starting with "SQ ". Therefore in order to make this work you just need to write a program which only prints the first line starting with "SQ " in each entry and skips the following SQ lines. Hope this helps! Best regards, Isabelle Wells F. Hoffmann-La Roche Ltd -----Original Message----- From: emboss-bounces at lists.open-bio.org [mailto:emboss-bounces at lists.open-bio.org] On Behalf Of Rozenbaum, Daniel (Biocceleration Inc) Sent: Wednesday, 6. February 2013 16:50 To: emboss at lists.open-bio.org Subject: [EMBOSS] Working with Geneseq databases Dear all, Does anyone have experience getting EMBOSS to work with the Geneseq database distributed by Thomson Reuters ( http://thomsonreuters.com/products_services/science/science_products/a-z/geneseq/ ) ? This database comes in "EMBL-like" format that uses some line codes that are not defined in EMBL format proper, which in our experiments has caused problems when, for example, trying to index these databases as EMBL-formatted. -- Daniel Rozenbaum Biocceleration, Inc. OCIO/Office of Application Engineering and Development/Patent System Division 600 Dulany St., Alexandria, VA 22314 From saidi34 at hushmail.com Tue Feb 12 12:44:01 2013 From: saidi34 at hushmail.com (saidi34 at hushmail.com) Date: Tue, 12 Feb 2013 12:44:01 -0500 Subject: [EMBOSS] =?utf-8?q?A_Ph=2ED=2E_Student=E2=80=99s_CRY_for_Help?= Message-ID: <20130212174401.A3F1FE6739@smtp.hushmail.com> A Ph.D. Student?s CRY for Help To: Prof. Hamid Arabnia, WORLDCOMP Coordinator, Professor of Computer Science, University of Georgia, USA Prof. Hamid Arabnia, I am a student from Africa and I am in the final stages of my Ph.D. work. I have a journal paper in ACM and a conference paper in WORLDCOMP. As per my university policy, I am required to have at least two research papers in peer-reviewed (refereed) international conferences or journals before I submit my synopsis/dissertation. While everything was fine, recently, WORLDCOMP was declared as a bogus conference with evidences and endorsements from scientists: https://sites.google.com/site/worlddump1 Also see http://worldcomp-fake-bogus.blogspot.com Now, my university officials have stopped me from submitting the dissertation stating that WORLDCOMP is not peer-reviewed due to the evidences in these websites. They said that WORLDCOMP is completely fake and that?s why you have not responded to the open challenge at https://sites.google.com/site/dumpconf or https://sites.google.com/site/moneycomp1 I sent many emails to you requesting to respond to the open challenge and prove that WORLDCOMP is not fake so that I can show your response to my university officials and convince them and submit my dissertation. I also asked you to email me the reviews for my paper (I never received them, although your acceptance email stated that the paper was reviewed by two experts) but you are not responding. Recall that when I met you in WORLDCOMP, you offered me a reference letter and invited me to organize a session in the next conference and promised free registration for my next paper if I get at least five registered papers fr om others. Now I am shocked with your silence. I am clueless on what to do as I will forfeit my student status unless I submit the dissertation soon. I am facing humiliation here. I was attracted by the keynote speakers, sponsors, tutorials, and University of Georgia name at WORLDCOMP website. Now I feel that I made a very critical mistake by submitting to WORLDCOMP. As the last resort, I am posting to this mailing list/forum (where WORLDCOMP details were published in the past I think) so that you understand the seriousness. I once again ask you to provide a detailed response at WORLDCOMP?s website and prove that it is not a fake (and also email me my paper reviews). I request you to focus on this issue than organizing the next conference (and create more victims like me). I hope you still have moral values. My elderly parents are dependent on me and I am crying for help. I openly beg your response! Respectfully, Saidi (this is my nickname and I am using it to avoid further humiliation. I know that you will easily identify me from this nickname and from my background mentioned above). To the forum/list owner: please understand my situation and publish this message and it will help other researchers to be more careful while choosing a conference. To the members: please help me getting a response from Prof. Arabnia. From peter.r.hoyt at okstate.edu Wed Feb 13 14:58:16 2013 From: peter.r.hoyt at okstate.edu (peter.r.hoyt at okstate.edu) Date: Wed, 13 Feb 2013 13:58:16 -0600 Subject: [EMBOSS] Stream Closed In-Reply-To: <20130212174401.A3F1FE6739@smtp.hushmail.com> References: <20130212174401.A3F1FE6739@smtp.hushmail.com> Message-ID: <511BF058.60606@okstate.edu> I'm trying to convert files using Seqret that are too large for the interactive webpage. I try to add my email, but still get a stream closed error. How can I request a large job run? -- Peter R. Hoyt, Ph. D. Director, Bioinformatics Certification Graduate Program, Oklahoma State University Department of Biochemistry and Molecular Biology 110FB Henry Bellmon Research Center (Shipping address: 246 Noble Research Center) Stillwater, OK 74078 (405) 744-6206 FAX (405) 744-7799 From ricepeterm at yahoo.co.uk Wed Feb 13 17:21:49 2013 From: ricepeterm at yahoo.co.uk (Peter Rice) Date: Wed, 13 Feb 2013 22:21:49 +0000 Subject: [EMBOSS] Stream Closed In-Reply-To: <511BF058.60606@okstate.edu> References: <20130212174401.A3F1FE6739@smtp.hushmail.com> <511BF058.60606@okstate.edu> Message-ID: <511C11FD.106@yahoo.co.uk> On 13/02/2013 19:58, peter.r.hoyt at okstate.edu wrote: > I'm trying to convert files using Seqret that are too large for the > interactive webpage. I try to add my email, but still get a stream > closed error. > > How can I request a large job run? Ummm... which webpage are you using? How large are the files? The simplest solution would be to install EMBOSS locally to convert the files. regards, Peter Rice EMBOSS Team From bernd.lentes at helmholtz-muenchen.de Thu Feb 14 06:56:00 2013 From: bernd.lentes at helmholtz-muenchen.de (Lentes, Bernd) Date: Thu, 14 Feb 2013 12:56:00 +0100 Subject: [EMBOSS] ./configure blaims about missing package although xorg-x11-proto-devel is installed - SOLVED In-Reply-To: <15785B7E063D464C86DD482FCAE4EBA5017F71493022@XCH11.scidom.de> References: <15785B7E063D464C86DD482FCAE4EBA5017F71493022@XCH11.scidom.de> Message-ID: <15785B7E063D464C86DD482FCAE4EBA5017F78CC0A22@XCH11.scidom.de> Bernd wrote: > > Hi, > > i'm new to EMBOSS and trying to install it for one of our > developers. We downloaded the current version, unpacked it > and started ./configure. It blaims about missing > xorg-x11-proto-devel, although it is installed: > > pc56846:~/EMBOSS-6.2.0 # rpm -q xorg-x11-proto-devel > xorg-x11-proto-devel-7.4-1.24.25.42 > > The exact error is: > X11 graphics have been selected but no X11 header files > have been found. > > This error usually happens on Linux/MacOSX distributions > where the optional X11 development files have not been installed. > On Linux RPM systems this package is usually called something > like xorg-x11-proto-devel whereas on Debian/Ubuntu it may > be called x-dev. On MacOSX installation DVDs the X11 files > can usually be found as an explicitly named optional > installation. > > > I tried version 6.2.0 and 6.5.7. Host is a SLES 11 SP1, 64bit. > I also tried "./configure --x-includes=/usr/include/X11/", > but it didn't suceed. > Hi, i found it out by myself. ./configure was searching for a file Xlib.h . This file is included in "xorg-x11-libX11-devel". After installing this packages and all necessary dependencies configure didn't blame any longer. I found the crucial hint in config.log . Bernd Helmholtz Zentrum M?nchen Deutsches Forschungszentrum f?r Gesundheit und Umwelt (GmbH) Ingolst?dter Landstr. 1 85764 Neuherberg www.helmholtz-muenchen.de Aufsichtsratsvorsitzende: MinDir?in B?rbel Brumme-Bothe Gesch?ftsf?hrer: Prof. Dr. G?nther Wess und Dr. Nikolaus Blum Registergericht: Amtsgericht M?nchen HRB 6466 USt-IdNr: DE 129521671 From Geetha.Vasudevan at bms.com Thu Feb 14 10:50:56 2013 From: Geetha.Vasudevan at bms.com (Vasudevan, Geetha) Date: Thu, 14 Feb 2013 10:50:56 -0500 Subject: [EMBOSS] EMBOSSWIN and JRE Message-ID: <4F3EC1CE7A305245A71338EEC51D821FCD2A8660D6@USHPWBMSCMP002.one.ads.bms.com> I am interested only in command prompt of EMBOSSWIN for Pepstats and IEP. Is it possible to install EMBOSSWIN without JRE? Is it a prerequisite? There might be some security issues in installing JRE. Thanks Geetha ________________________________ This message (including any attachments) may contain confidential, proprietary, privileged and/or private information. The information is intended to be for the use of the individual or entity designated above. If you are not the intended recipient of this message, please notify the sender immediately, and delete the message and any attachments. Any disclosure, reproduction, distribution or other use of this message or any attachments by an individual or entity other than the intended recipient is prohibited. From uludag at ebi.ac.uk Thu Feb 14 12:13:47 2013 From: uludag at ebi.ac.uk (Mahmut Uludag) Date: Thu, 14 Feb 2013 17:13:47 +0000 Subject: [EMBOSS] EMBOSSWIN and JRE In-Reply-To: <4F3EC1CE7A305245A71338EEC51D821FCD2A8660D6@USHPWBMSCMP002.one.ads.bms.com> References: <4F3EC1CE7A305245A71338EEC51D821FCD2A8660D6@USHPWBMSCMP002.one.ads.bms.com> Message-ID: <511D1B4B.4030708@ebi.ac.uk> Hi Geetha, > I am interested only in command prompt of EMBOSSWIN for Pepstats and IEP. > Is it possible to install EMBOSSWIN without JRE? Is it a prerequisite? It should be possible to use mEMBOSS command line programs without using its Java user interface. ftp://emboss.open-bio.org/pub/EMBOSS/windows/ I don't remember whether mEMBOSS installation requires JRE installed but I think it should not require. Mahmut From jttkim at googlemail.com Thu Feb 28 11:14:00 2013 From: jttkim at googlemail.com (Jan T Kim) Date: Thu, 28 Feb 2013 16:14:00 +0000 Subject: [EMBOSS] seqret segfault (refseq protein sequence, indexed with dbxflat) Message-ID: <20130228161359.GC4062@paxarchia.galaxy.uni> Dear All, I've run into a weird problem with seqret after downloading the complete protein refseq database and indexing that with dbxflat. The problem seems to be triggered by a rare condition, so far I've only encountered it with accession ZP_10312765: % seqret -feature -outseq=stdout -osformat=swiss ptest:ZP_10312765 Monitoring the seqret process using top, I noticed that the process grows to a size of 2g before segfaulting. Trying the same with ZP_10312766, the next record in the file, causes no problem. Also, -osformat=fasta and -osformat=genbank work with ZP_10312765, so the problem seems to be with outputting the swiss format. This happens on an Ubuntu 12.10 system (Linux 3.5.0-22-generic x86_64, emboss 6.4.0-4) and a Debian wheezy system (Linux 3.2.35-2 x86_64, emboss 6.4.0-2) as well. I attach a file containing the problematic refseq entry ZP_10312765 and the unproblematic next one, ZP_10312766. This should allow reproducing the problem as follows (please use this to check where I do something stupid or if you can spot anything broken in the ZP_10312765 record, but don't actually try to reproduce this unless you're confident you can hack & repair your ~/.embossrc and you understand the commands involved): (1) Put this into your ~/.embossrc, replacing "yourusername" as appropriate: SET ptestdir /home/yourusername/tmp/ptest db ptest [ type: p directory: $ptestdir indexdirectory: $ptestdir/index filename: *.gpff format: refseqp method: emboss release: "test" comment: "test protein database" ] (2) Run the following commands: mkdir ~/tmp/ptest mkdir ~/tmp/ptest/index # save or copy the attached ptest.gpff in ~/tmp/ptest cd ~/tmp/ptest/index dbxflat -dbname ptest -dbresource dbxresource -idformat refseq -directory ../ -filename '*.gpff' -statistics -fields id,ac,sv,des,key,org -compressed -outfile ptest.dbxflat cd ../.. seqret -feature -outseq=stdout -osformat=swiss ptest:ZP_10312765 The output I get on my terminal window is: Reads and writes (returns) sequences ID ZP_10312765 Reviewed; 498 AA. AC ZP_10312765; DT 31-DEC-1899, entry version 1. DE hypothetical protein FraQA3DRAFT_6339 [Frankia sp. QA3]. OS Frankia sp. QA3. RN [1] RP 1-498 RN [2] RP 1-498 KW . FT REGION 1 498 Frankia sp. QA3. QA3. taxon:710111. FT REGION 1 498 hypothetical protein. 53620. Segmentation fault I'd appreciate any help / comments. Best regards, Jan -- +- Jan T. Kim -------------------------------------------------------+ | email: jttkim at gmail.com | | WWW: http://www.jtkim.dreamhosters.com/ | *-----=< hierarchical systems are for files, not for humans >=-----* From sebastien.moretti at unil.ch Fri Feb 1 09:15:55 2013 From: sebastien.moretti at unil.ch (=?ISO-8859-1?Q?Moretti_S=E9bastien?=) Date: Fri, 01 Feb 2013 10:15:55 +0100 Subject: [EMBOSS] emma and clustalw2 In-Reply-To: <510A9DD1.4020303@ebi.ac.uk> References: <510A95FB.3040103@unil.ch> <510A9DD1.4020303@ebi.ac.uk> Message-ID: <510B87CB.9040400@unil.ch> Hi Mahmut, Thanks it works nicely this way. So, move back to external: "clustalw" and use EMBOSS_CLUSTALW variable. > Hi Sebastien, > > It looks if I set EMBOSS_CLUSTALW environment variable to point to > clustalw2 executable, as in the following example, i don't need to > modify the emma.acd file. > > export EMBOSS_CLUSTALW=~/esbin/clustalw-2.1/bin/clustalw2 > > Regards, > Mahmut > >> I try to use emma (v 6.5.7.0) with clustalw2 (v 2.1) on Linux x86_64. >> My environment contains both clustalw and clustalw2, that's why >> clustalw2 binary is called clustalw2. >> Accordingly I have changed this line in the emma.acd file (before >> compilation): >> external: "clustalw2" >> instead of >> external: "clustalw" >> >> >> When I try to run emma, I get this error message: >> >> Multiple sequence alignment (ClustalW wrapper) >> Warning: Cannot find 'clustalw', no ACD external definition found >> Error: Failed to open filename '00011120B' >> Problem writing out EMBOSS alignment file >> Error: File 'msf::00011120B' remove failed, error:2 'No such file or >> directory' -- S?bastien Moretti SIB Vital-IT EMBnet, Quartier Sorge - Genopode CH-1015 Lausanne, Switzerland Tel.: +41 (21) 692 4079/4221 http://www.vital-it.ch/ http://myhits.vital-it.ch/ From daniel.rozenbaum at USPTO.GOV Wed Feb 6 15:50:00 2013 From: daniel.rozenbaum at USPTO.GOV (Rozenbaum, Daniel (Biocceleration Inc)) Date: Wed, 6 Feb 2013 10:50:00 -0500 Subject: [EMBOSS] Working with Geneseq databases Message-ID: Dear all, Does anyone have experience getting EMBOSS to work with the Geneseq database distributed by Thomson Reuters ( http://thomsonreuters.com/products_services/science/science_products/a-z/geneseq/ ) ? This database comes in "EMBL-like" format that uses some line codes that are not defined in EMBL format proper, which in our experiments has caused problems when, for example, trying to index these databases as EMBL-formatted. -- Daniel Rozenbaum Biocceleration, Inc. OCIO/Office of Application Engineering and Development/Patent System Division 600 Dulany St., Alexandria, VA 22314 From isabelle.wells at roche.com Thu Feb 7 10:14:08 2013 From: isabelle.wells at roche.com (Wells, Isabelle) Date: Thu, 7 Feb 2013 11:14:08 +0100 Subject: [EMBOSS] Working with Geneseq databases In-Reply-To: References: Message-ID: <2489C38FDAFBFD41B59E3156253FFA6E0286DDDD55@rkamsem703.emea.roche.com> Hi Daniel, We index the geneseq databases in the EMBL format. The problem with Geneseq format is that each entry has several lines starting with "SQ ". Therefore in order to make this work you just need to write a program which only prints the first line starting with "SQ " in each entry and skips the following SQ lines. Hope this helps! Best regards, Isabelle Wells F. Hoffmann-La Roche Ltd? -----Original Message----- From: emboss-bounces at lists.open-bio.org [mailto:emboss-bounces at lists.open-bio.org] On Behalf Of Rozenbaum, Daniel (Biocceleration Inc) Sent: Wednesday, 6. February 2013 16:50 To: emboss at lists.open-bio.org Subject: [EMBOSS] Working with Geneseq databases Dear all, Does anyone have experience getting EMBOSS to work with the Geneseq database distributed by Thomson Reuters ( http://thomsonreuters.com/products_services/science/science_products/a-z/geneseq/ ) ? This database comes in "EMBL-like" format that uses some line codes that are not defined in EMBL format proper, which in our experiments has caused problems when, for example, trying to index these databases as EMBL-formatted. -- Daniel Rozenbaum Biocceleration, Inc. OCIO/Office of Application Engineering and Development/Patent System Division 600 Dulany St., Alexandria, VA 22314 _______________________________________________ EMBOSS mailing list EMBOSS at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss From daniel.rozenbaum at USPTO.GOV Thu Feb 7 14:27:57 2013 From: daniel.rozenbaum at USPTO.GOV (Rozenbaum, Daniel (Biocceleration Inc)) Date: Thu, 7 Feb 2013 09:27:57 -0500 Subject: [EMBOSS] Working with Geneseq databases In-Reply-To: <2489C38FDAFBFD41B59E3156253FFA6E0286DDDD55@rkamsem703.emea.roche.com> References: , <2489C38FDAFBFD41B59E3156253FFA6E0286DDDD55@rkamsem703.emea.roche.com> Message-ID: Hi Isabelle, Thanks a lot for your feedback. I might be doing something wrong, but even after I remove the extra SQ lines, dbiflat still fails with something like EMBOSS An error in embdbi.c at line 1569: Error in embDbiSortWriteFields, expected entry not found, last was 'BAD10932' Have you seen anything like this by any chance? Looking at the ".acnum_sort" dbiflat creates, it appears that dbiflat misinterprets some of the lines with non-standard line type codes like "PA", and appears to treat the strings in those lines as accession numbers. Not sure if my interpretation of what I'm seeing is correct, and whether this is what's causing the error I mentioned above. What I did try was to simply add the "CC" line type code at the beginning of any line whose line type code is not in EMBL standard. This seems to have done the trick, but I'm wondering if it's the best way to go. If it matters, we're using EMBOSS 6.4.0 . Many thanks, Daniel ________________________________________ From: emboss-bounces at lists.open-bio.org [emboss-bounces at lists.open-bio.org] On Behalf Of Wells, Isabelle [isabelle.wells at roche.com] Sent: Thursday, February 07, 2013 5:14 AM To: emboss at lists.open-bio.org Subject: Re: [EMBOSS] Working with Geneseq databases Hi Daniel, We index the geneseq databases in the EMBL format. The problem with Geneseq format is that each entry has several lines starting with "SQ ". Therefore in order to make this work you just need to write a program which only prints the first line starting with "SQ " in each entry and skips the following SQ lines. Hope this helps! Best regards, Isabelle Wells F. Hoffmann-La Roche Ltd -----Original Message----- From: emboss-bounces at lists.open-bio.org [mailto:emboss-bounces at lists.open-bio.org] On Behalf Of Rozenbaum, Daniel (Biocceleration Inc) Sent: Wednesday, 6. February 2013 16:50 To: emboss at lists.open-bio.org Subject: [EMBOSS] Working with Geneseq databases Dear all, Does anyone have experience getting EMBOSS to work with the Geneseq database distributed by Thomson Reuters ( http://thomsonreuters.com/products_services/science/science_products/a-z/geneseq/ ) ? This database comes in "EMBL-like" format that uses some line codes that are not defined in EMBL format proper, which in our experiments has caused problems when, for example, trying to index these databases as EMBL-formatted. -- Daniel Rozenbaum Biocceleration, Inc. OCIO/Office of Application Engineering and Development/Patent System Division 600 Dulany St., Alexandria, VA 22314 From saidi34 at hushmail.com Tue Feb 12 17:44:01 2013 From: saidi34 at hushmail.com (saidi34 at hushmail.com) Date: Tue, 12 Feb 2013 12:44:01 -0500 Subject: [EMBOSS] =?utf-8?q?A_Ph=2ED=2E_Student=E2=80=99s_CRY_for_Help?= Message-ID: <20130212174401.A3F1FE6739@smtp.hushmail.com> A Ph.D. Student?s CRY for Help To: Prof. Hamid Arabnia, WORLDCOMP Coordinator, Professor of Computer Science, University of Georgia, USA Prof. Hamid Arabnia, I am a student from Africa and I am in the final stages of my Ph.D. work. I have a journal paper in ACM and a conference paper in WORLDCOMP. As per my university policy, I am required to have at least two research papers in peer-reviewed (refereed) international conferences or journals before I submit my synopsis/dissertation. While everything was fine, recently, WORLDCOMP was declared as a bogus conference with evidences and endorsements from scientists: https://sites.google.com/site/worlddump1 Also see http://worldcomp-fake-bogus.blogspot.com Now, my university officials have stopped me from submitting the dissertation stating that WORLDCOMP is not peer-reviewed due to the evidences in these websites. They said that WORLDCOMP is completely fake and that?s why you have not responded to the open challenge at https://sites.google.com/site/dumpconf or https://sites.google.com/site/moneycomp1 I sent many emails to you requesting to respond to the open challenge and prove that WORLDCOMP is not fake so that I can show your response to my university officials and convince them and submit my dissertation. I also asked you to email me the reviews for my paper (I never received them, although your acceptance email stated that the paper was reviewed by two experts) but you are not responding. Recall that when I met you in WORLDCOMP, you offered me a reference letter and invited me to organize a session in the next conference and promised free registration for my next paper if I get at least five registered papers fr om others. Now I am shocked with your silence. I am clueless on what to do as I will forfeit my student status unless I submit the dissertation soon. I am facing humiliation here. I was attracted by the keynote speakers, sponsors, tutorials, and University of Georgia name at WORLDCOMP website. Now I feel that I made a very critical mistake by submitting to WORLDCOMP. As the last resort, I am posting to this mailing list/forum (where WORLDCOMP details were published in the past I think) so that you understand the seriousness. I once again ask you to provide a detailed response at WORLDCOMP?s website and prove that it is not a fake (and also email me my paper reviews). I request you to focus on this issue than organizing the next conference (and create more victims like me). I hope you still have moral values. My elderly parents are dependent on me and I am crying for help. I openly beg your response! Respectfully, Saidi (this is my nickname and I am using it to avoid further humiliation. I know that you will easily identify me from this nickname and from my background mentioned above). To the forum/list owner: please understand my situation and publish this message and it will help other researchers to be more careful while choosing a conference. To the members: please help me getting a response from Prof. Arabnia. From peter.r.hoyt at okstate.edu Wed Feb 13 19:58:16 2013 From: peter.r.hoyt at okstate.edu (peter.r.hoyt at okstate.edu) Date: Wed, 13 Feb 2013 13:58:16 -0600 Subject: [EMBOSS] Stream Closed In-Reply-To: <20130212174401.A3F1FE6739@smtp.hushmail.com> References: <20130212174401.A3F1FE6739@smtp.hushmail.com> Message-ID: <511BF058.60606@okstate.edu> I'm trying to convert files using Seqret that are too large for the interactive webpage. I try to add my email, but still get a stream closed error. How can I request a large job run? -- Peter R. Hoyt, Ph. D. Director, Bioinformatics Certification Graduate Program, Oklahoma State University Department of Biochemistry and Molecular Biology 110FB Henry Bellmon Research Center (Shipping address: 246 Noble Research Center) Stillwater, OK 74078 (405) 744-6206 FAX (405) 744-7799 From ricepeterm at yahoo.co.uk Wed Feb 13 22:21:49 2013 From: ricepeterm at yahoo.co.uk (Peter Rice) Date: Wed, 13 Feb 2013 22:21:49 +0000 Subject: [EMBOSS] Stream Closed In-Reply-To: <511BF058.60606@okstate.edu> References: <20130212174401.A3F1FE6739@smtp.hushmail.com> <511BF058.60606@okstate.edu> Message-ID: <511C11FD.106@yahoo.co.uk> On 13/02/2013 19:58, peter.r.hoyt at okstate.edu wrote: > I'm trying to convert files using Seqret that are too large for the > interactive webpage. I try to add my email, but still get a stream > closed error. > > How can I request a large job run? Ummm... which webpage are you using? How large are the files? The simplest solution would be to install EMBOSS locally to convert the files. regards, Peter Rice EMBOSS Team From bernd.lentes at helmholtz-muenchen.de Thu Feb 14 11:56:00 2013 From: bernd.lentes at helmholtz-muenchen.de (Lentes, Bernd) Date: Thu, 14 Feb 2013 12:56:00 +0100 Subject: [EMBOSS] ./configure blaims about missing package although xorg-x11-proto-devel is installed - SOLVED In-Reply-To: <15785B7E063D464C86DD482FCAE4EBA5017F71493022@XCH11.scidom.de> References: <15785B7E063D464C86DD482FCAE4EBA5017F71493022@XCH11.scidom.de> Message-ID: <15785B7E063D464C86DD482FCAE4EBA5017F78CC0A22@XCH11.scidom.de> Bernd wrote: > > Hi, > > i'm new to EMBOSS and trying to install it for one of our > developers. We downloaded the current version, unpacked it > and started ./configure. It blaims about missing > xorg-x11-proto-devel, although it is installed: > > pc56846:~/EMBOSS-6.2.0 # rpm -q xorg-x11-proto-devel > xorg-x11-proto-devel-7.4-1.24.25.42 > > The exact error is: > X11 graphics have been selected but no X11 header files > have been found. > > This error usually happens on Linux/MacOSX distributions > where the optional X11 development files have not been installed. > On Linux RPM systems this package is usually called something > like xorg-x11-proto-devel whereas on Debian/Ubuntu it may > be called x-dev. On MacOSX installation DVDs the X11 files > can usually be found as an explicitly named optional > installation. > > > I tried version 6.2.0 and 6.5.7. Host is a SLES 11 SP1, 64bit. > I also tried "./configure --x-includes=/usr/include/X11/", > but it didn't suceed. > Hi, i found it out by myself. ./configure was searching for a file Xlib.h . This file is included in "xorg-x11-libX11-devel". After installing this packages and all necessary dependencies configure didn't blame any longer. I found the crucial hint in config.log . Bernd Helmholtz Zentrum M?nchen Deutsches Forschungszentrum f?r Gesundheit und Umwelt (GmbH) Ingolst?dter Landstr. 1 85764 Neuherberg www.helmholtz-muenchen.de Aufsichtsratsvorsitzende: MinDir?in B?rbel Brumme-Bothe Gesch?ftsf?hrer: Prof. Dr. G?nther Wess und Dr. Nikolaus Blum Registergericht: Amtsgericht M?nchen HRB 6466 USt-IdNr: DE 129521671 From Geetha.Vasudevan at bms.com Thu Feb 14 15:50:56 2013 From: Geetha.Vasudevan at bms.com (Vasudevan, Geetha) Date: Thu, 14 Feb 2013 10:50:56 -0500 Subject: [EMBOSS] EMBOSSWIN and JRE Message-ID: <4F3EC1CE7A305245A71338EEC51D821FCD2A8660D6@USHPWBMSCMP002.one.ads.bms.com> I am interested only in command prompt of EMBOSSWIN for Pepstats and IEP. Is it possible to install EMBOSSWIN without JRE? Is it a prerequisite? There might be some security issues in installing JRE. Thanks Geetha ________________________________ This message (including any attachments) may contain confidential, proprietary, privileged and/or private information. The information is intended to be for the use of the individual or entity designated above. If you are not the intended recipient of this message, please notify the sender immediately, and delete the message and any attachments. Any disclosure, reproduction, distribution or other use of this message or any attachments by an individual or entity other than the intended recipient is prohibited. From uludag at ebi.ac.uk Thu Feb 14 17:13:47 2013 From: uludag at ebi.ac.uk (Mahmut Uludag) Date: Thu, 14 Feb 2013 17:13:47 +0000 Subject: [EMBOSS] EMBOSSWIN and JRE In-Reply-To: <4F3EC1CE7A305245A71338EEC51D821FCD2A8660D6@USHPWBMSCMP002.one.ads.bms.com> References: <4F3EC1CE7A305245A71338EEC51D821FCD2A8660D6@USHPWBMSCMP002.one.ads.bms.com> Message-ID: <511D1B4B.4030708@ebi.ac.uk> Hi Geetha, > I am interested only in command prompt of EMBOSSWIN for Pepstats and IEP. > Is it possible to install EMBOSSWIN without JRE? Is it a prerequisite? It should be possible to use mEMBOSS command line programs without using its Java user interface. ftp://emboss.open-bio.org/pub/EMBOSS/windows/ I don't remember whether mEMBOSS installation requires JRE installed but I think it should not require. Mahmut From jttkim at googlemail.com Thu Feb 28 16:14:00 2013 From: jttkim at googlemail.com (Jan T Kim) Date: Thu, 28 Feb 2013 16:14:00 +0000 Subject: [EMBOSS] seqret segfault (refseq protein sequence, indexed with dbxflat) Message-ID: <20130228161359.GC4062@paxarchia.galaxy.uni> Dear All, I've run into a weird problem with seqret after downloading the complete protein refseq database and indexing that with dbxflat. The problem seems to be triggered by a rare condition, so far I've only encountered it with accession ZP_10312765: % seqret -feature -outseq=stdout -osformat=swiss ptest:ZP_10312765 Monitoring the seqret process using top, I noticed that the process grows to a size of 2g before segfaulting. Trying the same with ZP_10312766, the next record in the file, causes no problem. Also, -osformat=fasta and -osformat=genbank work with ZP_10312765, so the problem seems to be with outputting the swiss format. This happens on an Ubuntu 12.10 system (Linux 3.5.0-22-generic x86_64, emboss 6.4.0-4) and a Debian wheezy system (Linux 3.2.35-2 x86_64, emboss 6.4.0-2) as well. I attach a file containing the problematic refseq entry ZP_10312765 and the unproblematic next one, ZP_10312766. This should allow reproducing the problem as follows (please use this to check where I do something stupid or if you can spot anything broken in the ZP_10312765 record, but don't actually try to reproduce this unless you're confident you can hack & repair your ~/.embossrc and you understand the commands involved): (1) Put this into your ~/.embossrc, replacing "yourusername" as appropriate: SET ptestdir /home/yourusername/tmp/ptest db ptest [ type: p directory: $ptestdir indexdirectory: $ptestdir/index filename: *.gpff format: refseqp method: emboss release: "test" comment: "test protein database" ] (2) Run the following commands: mkdir ~/tmp/ptest mkdir ~/tmp/ptest/index # save or copy the attached ptest.gpff in ~/tmp/ptest cd ~/tmp/ptest/index dbxflat -dbname ptest -dbresource dbxresource -idformat refseq -directory ../ -filename '*.gpff' -statistics -fields id,ac,sv,des,key,org -compressed -outfile ptest.dbxflat cd ../.. seqret -feature -outseq=stdout -osformat=swiss ptest:ZP_10312765 The output I get on my terminal window is: Reads and writes (returns) sequences ID ZP_10312765 Reviewed; 498 AA. AC ZP_10312765; DT 31-DEC-1899, entry version 1. DE hypothetical protein FraQA3DRAFT_6339 [Frankia sp. QA3]. OS Frankia sp. QA3. RN [1] RP 1-498 RN [2] RP 1-498 KW . FT REGION 1 498 Frankia sp. QA3. QA3. taxon:710111. FT REGION 1 498 hypothetical protein. 53620. Segmentation fault I'd appreciate any help / comments. Best regards, Jan -- +- Jan T. Kim -------------------------------------------------------+ | email: jttkim at gmail.com | | WWW: http://www.jtkim.dreamhosters.com/ | *-----=< hierarchical systems are for files, not for humans >=-----*