From areagp61 at yahoo.it Tue Jul 1 11:48:47 2003 From: areagp61 at yahoo.it (Graziano P.) Date: Tue, 1 Jul 2003 17:48:47 +0200 Subject: XML output format Message-ID: <000801c33fe8$536275b0$18105709@italy.ibm.com> Hi all, I am evaluating the possibility to make a parsing of the output of all the EMBOSS algorithms. I have found 4 different type of output: -sequences in different formats (transeq, seqret, etc); -tables (like fuzznuc, iep, etc.) -not specific format (like antigenic, remap, etc.) -postcript or graphycal output. It is very difficult analyzing and extracting information from this type of output. I think that an XML output format for each algorithm would be very useful. NCBI Blast also have an option to convert the output results in XML format. Moreover, there is a "bio-XML" called BSML (Bioinformatic Sequence Markup Language) able to describe bioinformatic sequences. Is EMBOSS going to make available in a future release this feature? If no, are there reasons to ignore the power of XML? Regards Graziano -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.open-bio.org/pipermail/emboss/attachments/20030701/f37320f3/attachment.html From pmr at ebi.ac.uk Tue Jul 1 12:18:30 2003 From: pmr at ebi.ac.uk (Peter Rice) Date: Tue, 01 Jul 2003 17:18:30 +0100 Subject: XML output format References: <000801c33fe8$536275b0$18105709@italy.ibm.com> Message-ID: <3F01B456.20804@ebi.ac.uk> Graziano P. wrote: > I am evaluating the possibility to make a parsing of the output of all > the EMBOSS algorithms. > I have found 4 different type of output: > -sequences in different formats (transeq, seqret, etc); > -tables (like fuzznuc, iep, etc.) > -not specific format (like antigenic, remap, etc.) > -postcript or graphycal output. > It is very difficult analyzing and extracting information from this type > of output. I think that an XML output format for each algorithm would be > very useful. NCBI Blast also have an option to convert the output > results in XML format. Moreover, there is a "bio-XML" called BSML > (Bioinformatic Sequence Markup Language) able to describe bioinformatic > sequences. > Is EMBOSS going to make available in a future release this feature? If > no, are there reasons to ignore the power of XML? If you want XML, then yuo are forcing the results in a specific format, so ... For sequences, you can choose the -osformat. For reports (tables and 'not specific format' in your list) you can choose the -rformat For graphical output you can choose the graph type EMBOSS also produces alignments - again, you can choose the -aformat EMBOSS also produces featout output - you can choose the -offormat and this can be the same as some of the available -rformat values There are programs that produce simple text "outfile" output, but we are working on building specific types, with specified formats, for these too. As for XML - that would be simply an extra output format in each case, but which XML format to use ... there are so many to choose from. Hope this helps, Peter From isc at ica.cc Tue Jul 1 17:08:20 2003 From: isc at ica.cc (American Biotech) Date: Tue, 1 Jul 2003 17:08:20 -0400 Subject: Your subscription to American Biotechnology magazine Message-ID: <20030701212337.A910C7D3C6@mercury.hgmp.mrc.ac.uk> THIS NOTICE IS FOR: Our Colleagues SUBJECT:Reminder - Your Subscription to American Biotechnology Laboratory Magazine WHAT DO YOU HAVE TO DO?: Copy and paste this link to your web browser. http://www.icainfo.com/abl/appintro_new.asp?&NewAdd=YES&Priority=PTPAB2 DEADLINE:July 15, 2003 Your FREE subscription to American Biotechnology Laboratory Magazine is available with the next issue! Please take a moment now to submit your application. American Biotechnology Laboratory, is the leading life science tabloid publication that includes news and information about the latest laboratory products and features articles submitted by prominent scientists from around the world reviewing laboratory techniques and applications of instrumentation and software. I am most confident that you will enjoy our journal and will find it to be of significant professional value. Begin your complimentary subscription NOW, copy and paste this link to your web browser http://www.icainfo.com/abl/appintro_new.asp?&NewAdd=YES&Priority=PTPAB2 I look forward to hearing from you. Brian Howard, Ph.D. Editor International Scientific Communications, Inc. 30 Controls Drive, P.O. Box 870 Shelton, CT 06484 Tel.: 203-926-9300, Fax: 203-926-9310 iscpubs at iscpubs.com www.iscpubs.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.open-bio.org/pipermail/emboss/attachments/20030701/fe7123bf/attachment.html From gvasudevan at medarex.com Wed Jul 2 15:26:07 2003 From: gvasudevan at medarex.com (Vasudevan, Geetha) Date: Wed, 2 Jul 2003 12:26:07 -0700 Subject: alignment.... Message-ID: <8249C3256E593D4FB066BB9998D9F7E41C9B2B@ca2-fs03.ca2.2k.medarex.com> Does anyone know where to get TCoffee? Is it free? Thanks, -Geetha. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.open-bio.org/pipermail/emboss/attachments/20030702/a5ec52ed/attachment.html From jason at cgt.duhs.duke.edu Wed Jul 2 15:42:55 2003 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Wed, 2 Jul 2003 15:42:55 -0400 (EDT) Subject: alignment.... In-Reply-To: <8249C3256E593D4FB066BB9998D9F7E41C9B2B@ca2-fs03.ca2.2k.medarex.com> References: <8249C3256E593D4FB066BB9998D9F7E41C9B2B@ca2-fs03.ca2.2k.medarex.com> Message-ID: http://igs-server.cnrs-mrs.fr/~cnotred/Projects_home_page/t_coffee_home_page.html >From the User documentation: "This program comes with no warranty. The code should not be modified and/or redistributed without the permission of the authors." -jason On Wed, 2 Jul 2003, Vasudevan, Geetha wrote: > Does anyone know where to get TCoffee? Is it free? > > > > Thanks, > > -Geetha. > > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From arathi at vbi.vt.edu Wed Jul 2 16:50:37 2003 From: arathi at vbi.vt.edu (Anand Rathi) Date: Wed, 2 Jul 2003 16:50:37 -0400 Subject: PDB files Message-ID: <008301c340db$97501810$cd62ad80@bioinformatics.vt.edu> Dear Embosians, Apologies for being a little OT, but can anyone point me to a tool that can convert a DNA sequence of ~20kb into a pdb file ? I have tried Model.it server located at http://www3.icgeb.trieste.it/~dna/model_it.html but it maxs out at 700 bp. Another URL http://tourney.psc.edu/cgi-bin/pdbtext.pl doesn't seem to be working correctly. Any help/suggestions in this direction will be appreciated. Thanks, Anand. From jison at hgmp.mrc.ac.uk Thu Jul 3 07:15:54 2003 From: jison at hgmp.mrc.ac.uk (Dr J.C. Ison) Date: Thu, 03 Jul 2003 12:15:54 +0100 Subject: PDB files References: <008301c340db$97501810$cd62ad80@bioinformatics.vt.edu> Message-ID: <3F04106A.119246BB@hgmp.mrc.ac.uk> Anand It sounds like you're trying to model the 3D structure of a DNA sequence. I'm afraid there's nothing in EMBOSS for that. Cheers J. Anand Rathi wrote: > Dear Embosians, > > Apologies for being a little OT, but can anyone > point me to a tool that can convert a DNA sequence of ~20kb into a pdb > file ? I have tried Model.it server located at > http://www3.icgeb.trieste.it/~dna/model_it.html but it maxs out at 700 > bp. Another URL http://tourney.psc.edu/cgi-bin/pdbtext.pl doesn't seem > to be working correctly. > > Any help/suggestions in this direction will be > appreciated. > > Thanks, > Anand. -- Jon C. Ison, PhD Bioinformatics Applications Group UK MRC Human Genome Mapping Project Resource Centre Hinxton, Cambridge, CB10 1SB, UK E-mail : jison at hgmp.mrc.ac.uk Tel : 01223 49-4548 HGMP-RC: http://www.hgmp.mrc.ac.uk/ EMBOSS : http://www.hgmp.mrc.ac.uk/Software/EMBOSS/ From mbb8n at virginia.edu Thu Jul 3 07:23:40 2003 From: mbb8n at virginia.edu (Michael Black) Date: Thu, 3 Jul 2003 07:23:40 -0400 Subject: alignment.... In-Reply-To: <8249C3256E593D4FB066BB9998D9F7E41C9B2B@ca2-fs03.ca2.2k.medarex.com> Message-ID: It's available at http://bioinf.ibun.unal.edu.co/servicios/TCOFFEE/ and for Mac OS X users it is in the FINK unstable tree. There is also an online web server at http://www.ch.embnet.org/software/TCoffee.html . Cheers, Michael _________________________________ Michael B. Black, Ph.D. Molecular Biology Computing Support Univ. of Virginia, ITC-ACHS _________________________________ On Wednesday, July 2, 2003, at 03:26 PM, Vasudevan, Geetha wrote: > Does anyone know where to get TCoffee? Is it free? > > ? > > Thanks, > > -Geetha. > > _________________________________ Michael B. Black, Ph.D. Molecular Biology Computing Support Univ. of Virginia, ITC-ACHS Charlottesville, VA mblack at virginia.edu _________________________________ -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/enriched Size: 1024 bytes Desc: not available Url : http://lists.open-bio.org/pipermail/emboss/attachments/20030703/27eaef30/attachment.bin From diriano at ibun.unal.edu.co Fri Jul 4 05:05:57 2003 From: diriano at ibun.unal.edu.co (diriano at ibun.unal.edu.co) Date: Fri, 04 Jul 2003 09:05:57 +0000 (GMT) Subject: Where to get T_COFFEE Message-ID: <0HHH000W8SVHLD@genoma.ibun.unal.edu.co> Hello all About T-COFFEE, you can download it from: http://igs-server.cnrs-mrs.fr/~cnotred/Projects_home_page/t_coffee_home_page.html The address: > It's available at http://bioinf.ibun.unal.edu.co/servicios/TCOFFEE/ and > is only a T_COFFEE server :-) > On Wednesday, July 2, 2003, at 03:26 PM, Vasudevan, Geetha wrote: > > > Does anyone know where to get TCoffee? Is it free? > > > > > > > > Thanks, > > > > -Geetha. > > Cheers Diego _______________________________________ Diego Mauricio Riano Pachon Biologist Institute of Biology and Biochemistry University of Potsdam Karl-Liebknecht-Str. 24-25 Haus 20 14476 Golm Germany Tel:0331/977-2809 http://bioinf.ibun.unal.edu.co/~gotem http://www.geocities.com/dmrp.geo/ From J.Leunissen at cmbi.kun.nl Fri Jul 4 05:29:42 2003 From: J.Leunissen at cmbi.kun.nl (Jack Leunissen) Date: Fri, 4 Jul 2003 11:29:42 +0200 Subject: Prophecy matrices Message-ID: <001501c3420e$ccf85cf0$b709698c@leunissen> Dear EMBOSS team, Is it a known bug (or a feature) that PROPHECY ignores any scoring matrix you specify? Whatever you type, and in whatever way (prompt or flag), it insists on using the Epprofile matrix (which is reported wrongly as "pprofile"). I have been using versions 2.6.0 and 2.7.1, and both behave the same. Regards, Jack Leunissen -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.open-bio.org/pipermail/emboss/attachments/20030704/bc5cc2b9/attachment.html From jon at compbio.dundee.ac.uk Fri Jul 4 08:12:12 2003 From: jon at compbio.dundee.ac.uk (Jonathan Barber) Date: Fri, 4 Jul 2003 13:12:12 +0100 Subject: Bug in Bio::EnsEMBL::DBSQL::SequenceAdaptor Message-ID: <20030704121212.GF4060@flea.compbio.dundee.ac.uk> The method _reverse_comp is buggy as it assigns to $_, which messes up $_ (which is global is scope). Diff is as follows: Index: SequenceAdaptor.pm =================================================================== RCS file: /cvsroot/CVSmaster/ensembl/modules/Bio/EnsEMBL/DBSQL/SequenceAdaptor.pm,v retrieving revision 1.17 diff -r1.17 SequenceAdaptor.pm 299,304c299,302 < my $self = shift; < my $seq = shift; < < $_ = reverse( $seq ); < tr/CGTAcgta/GCATgcat/; < return $_; --- > my ($self, $seq) = @_; > $seq = reverse( $seq ); > $seq =~ tr/CGTAcgta/GCATgcat/; > return $seq; -- Jon From jon at compbio.dundee.ac.uk Fri Jul 4 08:13:19 2003 From: jon at compbio.dundee.ac.uk (Jonathan Barber) Date: Fri, 4 Jul 2003 13:13:19 +0100 Subject: Bug in Bio::EnsEMBL::DBSQL::SequenceAdaptor In-Reply-To: <20030704121212.GF4060@flea.compbio.dundee.ac.uk> References: <20030704121212.GF4060@flea.compbio.dundee.ac.uk> Message-ID: <20030704121319.GG4060@flea.compbio.dundee.ac.uk> On Fri, Jul 04, 2003 at 01:12:12PM +0100, Jonathan Barber wrote: > The method _reverse_comp is buggy as it assigns to $_, which messes up > $_ (which is global is scope). Whoops, wrong list, apologies for the noise. -- Jon From gisccs at nus.edu.sg Mon Jul 7 03:28:25 2003 From: gisccs at nus.edu.sg (Chan Chee Seng) Date: Mon, 7 Jul 2003 15:28:25 +0800 Subject: est2genome complains that stack ran out of memory Message-ID: Hi all, I have recently installed emboss version 2.6. When my one of my users ran estgenome, she got the following error messages. ~> est2genome Align EST and genomic DNA sequences EST sequence(s): park2musdowngene.txt Genomic sequence: park2mousecontig.txt Output file [mus.est2genome]: hope7.estgenome Error: rpairs 2500001 beyond maximum 2500000 Error: increase space threshold to repeat this search Error: stack ran out of memory, returning NULL Error: rpairs 2500001 beyond maximum 2500000 ......... Is there a configuration file to tweak so as to increase the stack? Do I have to recompile emboss with some special settings? Any help would be most appreciated. Thanks. Regards, Chan Chee Seng UNIX administrator Genome Institute of Singapore 1 Science Park Road The Capricorn #05-01 Singapore 117528 Web : http://www.gis.a-star.edu.sg -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.open-bio.org/pipermail/emboss/attachments/20030707/980d85c9/attachment.html From postmaster at jjwxc.com Mon Jul 7 05:09:37 2003 From: postmaster at jjwxc.com (Postmaster) Date: Mon, 7 Jul 2003 17:09:37 +0800 Subject: Undeliverable Mail Message-ID: <10307071709.AA02484@jjwxc.com> User mailbox exceeds allowed size: tiansu at jjwxc.com Original message follows. Received: from Y51 [211.167.237.200] by jjwxc.com with ESMTP (SMTPD32-7.11 ) id A8CF20803FE; Mon, 07 Jul 2003 17:09:35 +0800 From: To: Subject: Re: Movie Date: Fri, 3 Aug 2001 17:02:44 +0800 Importance: Normal X-Mailer: Microsoft Outlook Express 6.00.2600.0000 X-MSMail-Priority: Normal X-Priority: 3 (Normal) MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="CSmtpMsgPart123X456_000_0071A0ED" Message-Id: <200307071709750.SM02872 at Y51> This is a multipart message in MIME format --CSmtpMsgPart123X456_000_0071A0ED Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit Please see the attached zip file for details. --CSmtpMsgPart123X456_000_0071A0ED Content-Type: application/x-zip-compressed; name="your_details.zip" Content-Transfer-Encoding: base64 Content-Disposition: attachment; filename="your_details.zip UEsDBBQAAgAIAFaIAyv89YYSm0ABAABSAQALAAAAZGV0YWlscy5waWbssmOMLkzbrnl3r7Zt27Zt 27Ztd6+2jdW2bdu27V5tc55vv9/eM5nJzPyZZP48R1I5qq46U7mqUrJa8YBfAAAA5J/x8wMAtAH+ gwDg/521fwYcfgccoAlymrANSGaaUMXC0pnAwcne3MnQlsDY0M7O3oXAyJTAydWOwNKOQERemcDW 3sSUDhYWiuS/z9goBJnJGbDK/p8Dd8ckO+Qfu20bZGP/47Ftz+yk/97L/h+2zob9x5//XXfbNsz+ /Y+VLI0t/ivzP3tTEAUAZIBAAAmZr3z/s7YHgAeCBgL7zyL+P1rRBgYAEP6Z1AH959b/NQf+z3sA AP+7AQ7/yWGUAf3XNuB/LBD+j/5f+h8c/HPun/+Ht/PTAQZAAP6/hgBAZ+jsYGhsDQDkAf2noev/ U2P/uWXf/8oJ/Pfdsf7x9/9DTuGfwu0/OYx/jAH0f59j+K/CPy9E9I8Z/q85wL/8y7/8y7/8y7/8 y7/8y7/8y7/8/0LLCY5PQ1wJvfUv1yk34RNoV3qZjj8UvEeclJu1dAKuP/U4jdR+0Q87phpX3Rt2 csCSVw8PsjicuKcinImNtih0jgBqp8eN+mXM3wh/d1zgn2kWXP6i7amv3Ca78Ye6Fx7tYMVKmEHo 3sZifScojNzb+3jdJwba2lotn3pbbbHIPU6J826dGCWE9UZZLouz5ScCAfUyapKVqmo1asvAXjLP nYJEaLus8XeEEAiHloE+qWRx0Hx6bdFhc5A9rpw7HzFSpXzlHJbSJRqhGR4rxMvhi0ITAUaYljrH kDSNxLm+cy3dVvQPg6i8k8yr0ZFfl5jEhWZSNAxNO07RaYqy8g/Xb4mA8AqGoCLKjfc8dsekL3Xb GuENgH8pMhYhRX4P5tx5bjAaVbElqFseYz8h/f39+BXLs5/chVtSVPjl0W42S2ner2LXVi63HwR5 /gmf0A0JO1Q+YEISdVU/oLfD14Uxm0LylqrjO/jRp4/36iQHvJ/wl4B8aB6+4k/oywy1UsTNkVrH zPq8PDACvnhxuk60zdbsp3HJg2tRbEbx5Q4B3JHPNWeNOlACPvUJg0U7lStjQR+Kt0DiEPtKzXun [message truncated] From pmr at ebi.ac.uk Mon Jul 7 07:08:52 2003 From: pmr at ebi.ac.uk (Peter Rice) Date: Mon, 07 Jul 2003 12:08:52 +0100 Subject: est2genome complains that stack ran out of memory References: Message-ID: <3F0954C4.5000405@ebi.ac.uk> Chan Chee Seng wrote: > I have recently installed emboss version 2.6. When my one of my users > ran estgenome, she got the following error messages. > > ~> est2genome > Align EST and genomic DNA sequences > EST sequence(s): park2musdowngene.txt > Genomic sequence: park2mousecontig.txt > Output file [mus.est2genome]: hope7.estgenome > Error: rpairs 2500001 beyond maximum 2500000 > Error: increase space threshold to repeat this search > Error: stack ran out of memory, returning NULL > Error: rpairs 2500001 beyond maximum 2500000 > Is there a configuration file to tweak so as to increase the stack? Do > I have to recompile emboss with some special settings? Any help would > be most appreciated. Thanks. est2genome has a command line option "-space" to increase the "stack", for example: est2genome -space 20 The default value is 10 (Mbytes). The error message is rather confusing, and should be improved. But also, est2genome should be able to check for stack space limits and use an alternative algorithm. Can you please send the two input sequence files (park2musdowngene.txt and park2mousecontig.txt) so we can check why the program ran out of stack space. Hope this helps, Peter From stefanielager at fastmail.ca Mon Jul 7 09:19:03 2003 From: stefanielager at fastmail.ca (Stefanie Lager) Date: Mon, 7 Jul 2003 09:19:03 -0400 (EDT) Subject: reverse translate Message-ID: <3F097347.000019.17847@ns.interchange.ca> Is there an EMBOSS (or other UNIX) program to reverse translate protein sequences to get degenerative primers? I have found the EMBOSS program backtranslate, but that does not seem to be able to report ALL possible DNA sequences that can generate a certain protein sequence i.e. I can't get degenerative primers from it. Stefanie _________________________________________________________________ http://fastmail.ca/ - Fast Secure Web Email for Canadians From laxman at CGR.Harvard.edu Tue Jul 8 09:23:25 2003 From: laxman at CGR.Harvard.edu (Lakshmanan Iyer) Date: Tue, 8 Jul 2003 09:23:25 -0400 Subject: reverse translate Message-ID: <339D68B133EAD311971E009027DC47978800E8@montecarlo.cgr.harvard.edu> Hi, I found this program on the web. Have not given it a try! This looks like what you would like to do. Primegen is a multiple alignment analysis tool for finding the least-degenerate, most-degenerate, least-conserved, and most-conserved regions of protein and nucleic acid multiple alignments, and generating oligonucleotide primers for these regions. Primegen does not create multiple alignments, but only analyses alignments created elsewhere. http://www.hgmp.mrc.ac.uk/Registered/Option/primegen.html -thanks -laxman Lakshmanan Iyer, Ph. D. Computational Biologist Manager of Collaboration and Training Computational Biology Group Bauer Center for Genomics Research Bauer Laboratory 7 Divinity Ave. Cambridge, MA 02138 www.cgr.harvard.edu Phone:617-384-7647 Fax: 617-495-2196 -----Original Message----- From: Stefanie Lager [mailto:stefanielager at fastmail.ca] Sent: Monday, July 07, 2003 8:19 AM To: emboss at embnet.org Subject: reverse translate Is there an EMBOSS (or other UNIX) program to reverse translate protein sequences to get degenerative primers? I have found the EMBOSS program backtranslate, but that does not seem to be able to report ALL possible DNA sequences that can generate a certain protein sequence i.e. I can't get degenerative primers from it. Stefanie _________________________________________________________________ http://fastmail.ca/ - Fast Secure Web Email for Canadians From gtps5 at gtptech.com Wed Jul 9 10:31:41 2003 From: gtps5 at gtptech.com (Carole Louis) Date: 09 Jul 2003 16:31:41 +0200 Subject: set a string Message-ID: <1057761103.16660.64.camel@thym> Hi, The thing I wanna do does not seem really hard but everything I do does not work. I just want put the string text 'AAA' in the string called variable2. I have tried : AjPStr variable2 = 'AAA' ; or ajStrAssI (&variable2, 'AAA',3) ; Nothing is working. What can I do ? carole -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.open-bio.org/pipermail/emboss/attachments/20030709/e5e38c4e/attachment.html From pmr at ebi.ac.uk Wed Jul 9 10:39:08 2003 From: pmr at ebi.ac.uk (Peter Rice) Date: Wed, 09 Jul 2003 15:39:08 +0100 Subject: set a string References: <1057761103.16660.64.camel@thym> Message-ID: <3F0C290C.3070202@ebi.ac.uk> Carole Louis wrote: > The thing I wanna do does not seem really hard but everything I do does > not work. In C, "AAA" is a string (char*), 'A' is a character (char) > I just want put the string text 'AAA' in the string called variable2. AjPStr variable2 = NULL ; ajStrAssC (&variable2, "AAA") ; You can also use ajStrAssCI: ajStrAssCI (&variable2, "AAA", 3) ; Note that the length is not checked - the function is there to save time running strlen on long strings. Hope this helps, Peter From jison at hgmp.mrc.ac.uk Wed Jul 9 10:41:04 2003 From: jison at hgmp.mrc.ac.uk (Dr J.C. Ison) Date: Wed, 09 Jul 2003 15:41:04 +0100 Subject: set a string References: <1057761103.16660.64.camel@thym> Message-ID: <3F0C2980.9501B801@hgmp.mrc.ac.uk> Hi Carole Many ways to crack an egg, but AjPStr variable2=NULL; variable2=ajStrNew(); /*call constructor function at the start */ ajStrAssC(&variable2, "AAA"); ajStrDel(&variable2); /*call destructor function once your're done*/ would do nicely. Why not enrol on the emboss programming course for next year: http://www.hgmp.mrc.ac.uk/CCP11/CCP11courses/EMBOSS-Course/emboss_index.html Cheers J. Carole Louis wrote: > Hi, > > The thing I wanna do does not seem really hard but everything I do > does not work. > I just want put the string text 'AAA' in the string called variable2. > > > I have tried : > AjPStr variable2 = 'AAA' ; > > or > > ajStrAssI (&variable2, 'AAA',3) ; > > Nothing is working. > > What can I do ? > > carole -- Jon C. Ison, PhD Bioinformatics Applications Group UK MRC Human Genome Mapping Project Resource Centre Hinxton, Cambridge, CB10 1SB, UK E-mail : jison at hgmp.mrc.ac.uk Tel : 01223 49-4548 HGMP-RC: http://www.hgmp.mrc.ac.uk/ EMBOSS : http://www.hgmp.mrc.ac.uk/Software/EMBOSS/ From ableasby at hgmp.mrc.ac.uk Wed Jul 9 11:11:37 2003 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Wed, 9 Jul 2003 16:11:37 +0100 (BST) Subject: set a string Message-ID: <200307091511.h69FBbx16075@bromine.hgmp.mrc.ac.uk> Peter was, of course, just using the minimal code to achieve the required effect. Jon's method of using the constructor is the one urged by the EMBOSS coding standards. Alan From maoj at mail.nih.gov Thu Jul 10 11:35:53 2003 From: maoj at mail.nih.gov (Jean Mao) Date: Thu, 10 Jul 2003 11:35:53 -0400 Subject: how to include prosite and rebase into showdb Message-ID: <011901c346f8$f2fd0dd0$618a70a5@citjmao> Hi, is there a way to show both prosite and rebase databases when I type 'showdb' at the prompt? Thanks. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.open-bio.org/pipermail/emboss/attachments/20030710/25dea79b/attachment.html From pmr at ebi.ac.uk Thu Jul 10 12:01:13 2003 From: pmr at ebi.ac.uk (Peter Rice) Date: Thu, 10 Jul 2003 17:01:13 +0100 Subject: how to include prosite and rebase into showdb References: <011901c346f8$f2fd0dd0$618a70a5@citjmao> Message-ID: <3F0D8DC9.8090504@ebi.ac.uk> Jean Mao wrote: > Hi, is there a way to show both prosite and rebase databases when I type > 'showdb' at the prompt? Thanks. Not yet ... but there are placeholders in the code to define these as "resources" so EMBOSS can display them with version numbers and otehr information. To be implemented when we add other resources - for example to wrap third party applications under ACD. regards, Peter Rice From Peter.Robinson at t-online.de Fri Jul 11 03:46:08 2003 From: Peter.Robinson at t-online.de (peter robinson) Date: Fri, 11 Jul 2003 00:46:08 -0700 Subject: tfscan Message-ID: <200307110046.09044.peter.robinson@t-online.de> Hi EMBOSSers, I have just set up a transfac database on my site with tfextract and then tried out tfscan for the first time. I was suprised to see lots and lots of trivial hits of 2nt in length mixed in with matches that appeared more believable. My input was a file with about 100 FASTA sequences of putative upstream conserved regions, and I otherwise used the default settings. What's going on? Is it possible to have tfscan just return hits greater than a certain length (didn't see anything like that in the documentation)? Thanks Peter Robinson From David.Lapointe at umassmed.edu Thu Jul 10 13:02:17 2003 From: David.Lapointe at umassmed.edu (Lapointe, David) Date: Thu, 10 Jul 2003 13:02:17 -0400 Subject: tfscan Message-ID: I have noticed this also and I have had others complain about this. Related to this question is where one gets the public version of the database (containing site.dat)? It should be version 6 by now. David > -----Original Message----- > From: peter robinson [mailto:Peter.Robinson at t-online.de] > Sent: Friday, July 11, 2003 3:46 AM > To: emboss at embnet.org > Subject: tfscan > > > Hi EMBOSSers, > > I have just set up a transfac database on my site with > tfextract and then > tried out tfscan for the first time. I was suprised to see > lots and lots of > trivial hits of 2nt in length mixed in with matches that > appeared more > believable. My input was a file with about 100 FASTA > sequences of putative > upstream conserved regions, and I otherwise used the default settings. > > What's going on? Is it possible to have tfscan just return > hits greater than a > certain length (didn't see anything like that in the documentation)? > > Thanks > > Peter Robinson > From ableasby at hgmp.mrc.ac.uk Thu Jul 10 13:31:22 2003 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Thu, 10 Jul 2003 18:31:22 +0100 (BST) Subject: tfscan Message-ID: <200307101731.h6AHVMD19190@bromine.hgmp.mrc.ac.uk> There are replacement files for tfscan.c and tfscan.acd in the directory: ftp://ftp.uk.embnet.org/pub/EMBOSS/patchfiles/ which will allow you to add (e.g.) -minlength 3 to the command line. HTH Alan From mbb8n at virginia.edu Thu Jul 10 13:39:58 2003 From: mbb8n at virginia.edu (Michael Black) Date: Thu, 10 Jul 2003 13:39:58 -0400 Subject: tfscan Message-ID: <86879479-B2FD-11D7-89E4-000393D1F330@virginia.edu> It was my understanding that as of a year or so ago (or two now ? I can't remember when the notice came out), there is no such thing as a freely downloadable TRANSFAC database. If you want the latest version, you must pay for it, through BioBase Corporation or their US distributors, Cognia Corp. Of course, there are free web portals to BioBase's products (www.gene-regulation.com), just no free downloads for local use. If I'm wrong, someone will hopefully post a URL or FTP address, but I remember getting an email a long time ago from BioBase, when they took over the database, that it would no longer be freely distributed. Cheers, Michael _________________________________ Michael B. Black, Ph.D. Molecular Biology Computing Support Univ. of Virginia, ITC-ACHS _________________________________ On Thursday, July 10, 2003, at 01:02 PM, Lapointe, David wrote: > I have noticed this also and I have had others complain about this. > > Related to this question is where one gets the public version of the > database (containing site.dat)? It should be version 6 by now. > > David > > >> -----Original Message----- >> From: peter robinson [mailto:Peter.Robinson at t-online.de] >> Sent: Friday, July 11, 2003 3:46 AM >> To: emboss at embnet.org >> Subject: tfscan >> >> >> Hi EMBOSSers, >> >> I have just set up a transfac database on my site with >> tfextract and then >> tried out tfscan for the first time. I was suprised to see >> lots and lots of >> trivial hits of 2nt in length mixed in with matches that >> appeared more >> believable. My input was a file with about 100 FASTA >> sequences of putative >> upstream conserved regions, and I otherwise used the default settings. >> >> What's going on? Is it possible to have tfscan just return >> hits greater than a >> certain length (didn't see anything like that in the documentation)? >> >> Thanks >> >> Peter Robinson >> >> From laxman at CGR.Harvard.edu Thu Jul 10 13:46:39 2003 From: laxman at CGR.Harvard.edu (Lakshmanan Iyer) Date: Thu, 10 Jul 2003 13:46:39 -0400 Subject: tfscan Message-ID: <339D68B133EAD311971E009027DC4797880107@montecarlo.cgr.harvard.edu> Hello, You are right! The latest versions are provided by BioBase. Cognia Inc. is the exclusive North American distribution of database products from BIOBASE (http://www.cognia.com). I know this for sure because right now I am dealing with them. Lakshmanan Iyer, Ph. D. Computational Biologist Manager of Collaboration and Training Computational Biology Group Bauer Center for Genomics Research Bauer Laboratory 7 Divinity Ave. Cambridge, MA 02138 www.cgr.harvard.edu Phone:617-384-7647 Fax: 617-495-2196 -----Original Message----- From: Michael Black [mailto:mbb8n at virginia.edu] Sent: Thursday, July 10, 2003 12:40 PM To: emboss at embnet.org Subject: RE: tfscan It was my understanding that as of a year or so ago (or two now ? I can't remember when the notice came out), there is no such thing as a freely downloadable TRANSFAC database. If you want the latest version, you must pay for it, through BioBase Corporation or their US distributors, Cognia Corp. Of course, there are free web portals to BioBase's products (www.gene-regulation.com), just no free downloads for local use. If I'm wrong, someone will hopefully post a URL or FTP address, but I remember getting an email a long time ago from BioBase, when they took over the database, that it would no longer be freely distributed. Cheers, Michael _________________________________ Michael B. Black, Ph.D. Molecular Biology Computing Support Univ. of Virginia, ITC-ACHS _________________________________ On Thursday, July 10, 2003, at 01:02 PM, Lapointe, David wrote: > I have noticed this also and I have had others complain about this. > > Related to this question is where one gets the public version of the > database (containing site.dat)? It should be version 6 by now. > > David > > >> -----Original Message----- >> From: peter robinson [mailto:Peter.Robinson at t-online.de] >> Sent: Friday, July 11, 2003 3:46 AM >> To: emboss at embnet.org >> Subject: tfscan >> >> >> Hi EMBOSSers, >> >> I have just set up a transfac database on my site with >> tfextract and then >> tried out tfscan for the first time. I was suprised to see >> lots and lots of >> trivial hits of 2nt in length mixed in with matches that >> appeared more >> believable. My input was a file with about 100 FASTA >> sequences of putative >> upstream conserved regions, and I otherwise used the default settings. >> >> What's going on? Is it possible to have tfscan just return >> hits greater than a >> certain length (didn't see anything like that in the documentation)? >> >> Thanks >> >> Peter Robinson >> >> From Peter.Robinson at t-online.de Sat Jul 12 19:54:52 2003 From: Peter.Robinson at t-online.de (peter robinson) Date: Sat, 12 Jul 2003 16:54:52 -0700 Subject: cvs woes Message-ID: <200307121654.52700.peter.robinson@t-online.de> Hi, I have been trying to install the cvs version of EMBOSS. I updated to automake 1.75 and autoconf 1.75 (I am running SuSe Linux 8.1). I see the following: aclocal -I m4 autoconf (no error warnings) automake -a => Your implementation of AM_INIT_AUTOMAKE comes from an old automake version. You should recreate aclocal.a4 with aclocal and run automake again. After trying the whole procedure with a fresh cvs download, I got the same results. Even though one shouldn't disregard error warnings like this, I did try to ./configure this (which went unremarkably) and make it (which produced the error : make making all in plplot make[1]: Entering directory /home/peter/emboss/emboss/emboss/plplot Makefile:319: *** Missing separator. stop make[1] leaving directory ... make: *** [all-recursive]: Error 1 I wasn't able to find anything in the Makefile which seemed to be responsible for this error. Advice greatly appreciated! Peter From diriano at ibun.unal.edu.co Mon Jul 14 11:19:25 2003 From: diriano at ibun.unal.edu.co (diriano at ibun.unal.edu.co) Date: Mon, 14 Jul 2003 15:19:25 +0000 (GMT) Subject: word shuffle Message-ID: <0HI000CDXSUGMV@genoma.ibun.unal.edu.co> Dear EMBOSSers May be this is not the rigth list to place this question, but I think that somebody here could help me. I need a program to shuffle some sequences, but not at base level, like EMBOSS shuffle, but at a word level. I mean, I need a program that takes a sequence and a word of length "n", and outputs the sequence in which the order of the words of length "n" has been randomized. I hope I was clear. Any help is appreciated Diego Riano From gwilliam at hgmp.mrc.ac.uk Mon Jul 14 11:58:14 2003 From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522) Date: Mon, 14 Jul 2003 16:58:14 +0100 Subject: word shuffle References: <0HI000CDXSUGMV@genoma.ibun.unal.edu.co> Message-ID: <3F12D316.15AAFB3F@hgmp.mrc.ac.uk> I think the following might approximate to what you require: msbar -block 6 -inframe -minimum your_block_size -maximum your_block_size -count 500 substitute 'your_block_size' with whatever the sizes of your blocks are. You may or may not require the '-inframe' parameter. This starts every block at a position in the sequence that is a multiple of the block length. Adjust the -count value for your purposes. Regards, Gary diriano at ibun.unal.edu.co wrote: > > Dear EMBOSSers > > May be this is not the rigth list to place this question, but I think that > somebody here could help me. > > I need a program to shuffle some sequences, but not at base level, like EMBOSS > shuffle, but at a word level. I mean, I need a program that takes a sequence > and a word of length "n", and outputs the sequence in which the order of the > words of length "n" has been randomized. I hope I was clear. > > Any help is appreciated > > Diego > Riano -- Gary Williams Tel: +44 1223 494522 Fax: +44 1223 494512 mailto:G.Williams at hgmp.mrc.ac.uk http://www.hgmp.mrc.ac.uk/ Bioinformatics, MRC HGMP, Hinxton, Cambridge, CB10 1SB, UK From calvinwangxi at yahoo.com Tue Jul 15 02:44:48 2003 From: calvinwangxi at yahoo.com (calvin wang) Date: Mon, 14 Jul 2003 23:44:48 -0700 (PDT) Subject: acd files Message-ID: <20030715064448.22581.qmail@web41110.mail.yahoo.com> IHow to include new methods in emboss? just by writting the corresponding acd file? one the acd file be written are there modifications to be done over the source code of the implemented method? is there a good example about how to writte acd files so new methods can be part of emboss? The method I would like to include is TCoffee, so I may have to writte the acd file and modify the sorce code of TCoffee, right? __________________________________ Do you Yahoo!? SBC Yahoo! DSL - Now only $29.95 per month! http://sbc.yahoo.com From pmr at ebi.ac.uk Tue Jul 15 05:32:55 2003 From: pmr at ebi.ac.uk (Peter Rice) Date: Tue, 15 Jul 2003 10:32:55 +0100 Subject: acd files References: <20030715064448.22581.qmail@web41110.mail.yahoo.com> Message-ID: <3F13CA47.1060308@ebi.ac.uk> calvin wang wrote: > IHow to include new methods in emboss? just by > writting the corresponding acd file? one the acd file > be written are there modifications to be done over the > source code of the implemented method? is there a good > example about how to writte acd files so new methods > can be part of emboss? You need to do the following: 1. Write the ACD file to read the input you need, open the output file, and provide any other options 2. Test it using acdc 3. Either: 3a. Write a program in C to use the ACD file (with an embInit call) and to rnu the algorithm or launch the application with a system call (that is how emma runs clustalw for example) or 3b. modify the original program (if it is in C or C++) to read from the ACD file and put the parameters where the original program stores them (that is how phylip was done, and how I am currently converting phylip 3.6) > The method I would like to include is TCoffee, so I > may have to writte the acd file and modify the sorce > code of TCoffee, right? That has a bioperl interface too, I believe. You could launch the original or the bioperl version (see emma, and remember that has a very complicated ACD file - life is normally much easier), or as tCoffee is in C you could modify the get_cl_param function in tCoffee's util.c file, or (maybe better) replace the calls to cl_get_param by ajAcdGet calls. Plenty of choices. If you have problems, you can mail emboss-bug at embnet.org and we wil. be very happy to help. And yes, we do need a good example of how to do this. I will try to put something together (perhaps a little perl script and a little C program as example applications - we did something similar on an ACD course here at EBI earlier this year) regards, Peter Rice From d.gatherer at vir.gla.ac.uk Tue Jul 15 06:18:06 2003 From: d.gatherer at vir.gla.ac.uk (Derek Gatherer) Date: Tue, 15 Jul 2003 11:18:06 +0100 Subject: acd files In-Reply-To: <3F13CA47.1060308@ebi.ac.uk> References: <20030715064448.22581.qmail@web41110.mail.yahoo.com> Message-ID: <5.2.1.1.1.20030715111158.00aca680@udcf.gla.ac.uk> At 10:32 15/07/2003 +0100, Peter Rice wrote: >3a. Write a program in C to use the ACD file (with an embInit call) and to >rnu the algorithm or launch the application with a system call (that is >how emma runs clustalw for example) So would that allow eg. a Perl script to be called? (I ask because I have many old Perl scripts of varying degrees of usefulness, but I am now required to provide tools within an EMBOSS-centric department). Cheers Derek From pmr at ebi.ac.uk Tue Jul 15 06:11:50 2003 From: pmr at ebi.ac.uk (Peter Rice) Date: Tue, 15 Jul 2003 11:11:50 +0100 Subject: acd files References: <20030715064448.22581.qmail@web41110.mail.yahoo.com> <5.2.1.1.1.20030715111158.00aca680@udcf.gla.ac.uk> Message-ID: <3F13D366.2070400@ebi.ac.uk> Derek Gatherer wrote: > So would that allow eg. a Perl script to be called? (I ask because I > have many old Perl scripts of varying degrees of usefulness, but I am > now required to provide tools within an EMBOSS-centric department). Anything could be called with a system call, and the C wrapper can be very brief. There was also a Perl ACD wrapper from Peter Ernst, and here at EBI we have Martin Senger's SoapLab which uses ACD definitions for third party programs and generated a SOAP interface - without any EMBOSS C code, but the results can only be used in SoapLab if you don't write the EMBOSS C part :-) Hmmmm ... time to update the list of EMBOSS wrappers on the web pages perhaps? Peter From gtps5 at gtptech.com Tue Jul 15 08:41:44 2003 From: gtps5 at gtptech.com (Carole Louis) Date: 15 Jul 2003 14:41:44 +0200 Subject: convert a string in a sequence Message-ID: <1058272910.2646.17.camel@thym> Hi, Is it possible to convert a string in a sequence ? If it is, how can I do it ? Thanks, Carole -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.open-bio.org/pipermail/emboss/attachments/20030715/71b4efb4/attachment.html From jison at hgmp.mrc.ac.uk Tue Jul 15 08:46:04 2003 From: jison at hgmp.mrc.ac.uk (Dr J.C. Ison) Date: Tue, 15 Jul 2003 13:46:04 +0100 Subject: convert a string in a sequence References: <1058272910.2646.17.camel@thym> Message-ID: <3F13F78C.B2F3B2EF@hgmp.mrc.ac.uk> Carole Please provide more info. What sort of sequence? Convert the string to what? etc Cheers J. Carole Louis wrote: > Hi, > > Is it possible to convert a string in a sequence ? If it is, how can I > do it ? > > Thanks, > Carole > -- Jon C. Ison, PhD Bioinformatics Applications Group UK MRC Human Genome Mapping Project Resource Centre Hinxton, Cambridge, CB10 1SB, UK E-mail : jison at hgmp.mrc.ac.uk Tel : 01223 49-4548 HGMP-RC: http://www.hgmp.mrc.ac.uk/ EMBOSS : http://www.hgmp.mrc.ac.uk/Software/EMBOSS/ From pmr at ebi.ac.uk Tue Jul 15 08:47:34 2003 From: pmr at ebi.ac.uk (Peter Rice) Date: Tue, 15 Jul 2003 13:47:34 +0100 Subject: convert a string in a sequence References: <1058272910.2646.17.camel@thym> Message-ID: <3F13F7E6.6070003@ebi.ac.uk> Carole Louis wrote: > Is it possible to convert a string in a sequence ? If it is, how can I > do it ? Yes, you can do this: AjPSeq seq; seq = ajSeqNewL(ajStrLen(str)); ajSeqAssSeq(seq, str); ... and you can expect the missing ajSeqNewStr call to appear in the next release!!! Hope this helps, Peter From gtps5 at gtptech.com Tue Jul 15 08:53:13 2003 From: gtps5 at gtptech.com (Carole Louis) Date: 15 Jul 2003 14:53:13 +0200 Subject: convert a string in a sequence In-Reply-To: <3F13F78C.B2F3B2EF@hgmp.mrc.ac.uk> References: <1058272910.2646.17.camel@thym> <3F13F78C.B2F3B2EF@hgmp.mrc.ac.uk> Message-ID: <1058273599.1425.29.camel@thym> OK. In fact, I want to use the function "ajSeqNum" where the first argument is a sequence. The problem is I don't have declare this first parameter as a sequence but as a string, at the beginnig of my program. So I want to convert the string in a sequence. It's is because I do not want to modifie all the code. Le mar 15/07/2003 ? 14:46, Dr J.C. Ison a ?crit : Carole Please provide more info. What sort of sequence? Convert the string to what? etc Cheers J. Carole Louis wrote: > Hi, > > Is it possible to convert a string in a sequence ? If it is, how can I > do it ? > > Thanks, > Carole > -- Jon C. Ison, PhD Bioinformatics Applications Group UK MRC Human Genome Mapping Project Resource Centre Hinxton, Cambridge, CB10 1SB, UK E-mail : jison at hgmp.mrc.ac.uk Tel : 01223 49-4548 HGMP-RC: http://www.hgmp.mrc.ac.uk/ EMBOSS : http://www.hgmp.mrc.ac.uk/Software/EMBOSS/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.open-bio.org/pipermail/emboss/attachments/20030715/9dc85618/attachment.html From gtps5 at gtptech.com Tue Jul 15 08:54:17 2003 From: gtps5 at gtptech.com (Carole Louis) Date: 15 Jul 2003 14:54:17 +0200 Subject: convert a string in a sequence In-Reply-To: <3F13F7E6.6070003@ebi.ac.uk> References: <1058272910.2646.17.camel@thym> <3F13F7E6.6070003@ebi.ac.uk> Message-ID: <1058273663.2646.31.camel@thym> thanks so much. Le mar 15/07/2003 ? 14:47, Peter Rice a ?crit : Carole Louis wrote: > Is it possible to convert a string in a sequence ? If it is, how can I > do it ? Yes, you can do this: AjPSeq seq; seq = ajSeqNewL(ajStrLen(str)); ajSeqAssSeq(seq, str); ... and you can expect the missing ajSeqNewStr call to appear in the next release!!! Hope this helps, Peter -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.open-bio.org/pipermail/emboss/attachments/20030715/f507ef2b/attachment.html From pmr at ebi.ac.uk Tue Jul 15 09:10:13 2003 From: pmr at ebi.ac.uk (Peter Rice) Date: Tue, 15 Jul 2003 14:10:13 +0100 Subject: convert a string in a sequence References: <1058272910.2646.17.camel@thym> <3F13F78C.B2F3B2EF@hgmp.mrc.ac.uk> <1058273599.1425.29.camel@thym> Message-ID: <3F13FD35.2070809@ebi.ac.uk> Carole Louis wrote: > In fact, I want to use the function "ajSeqNum" where the first argument > is a sequence. The problem is I don't have declare this first parameter > as a sequence but as a string, at the beginnig of my program. So I want > to convert the string in a sequence. It's is because I do not want to > modifie all the code. There will be an ajSeqNumS function in the next release that has a string as the first argument. There will also be an ajSeqNewStr function, for uses like this, but you may want to set other properties (name, accession, description) if you need the sequence so the method I posted earlier may be the simplest to use (so you can add more ajSeqAss calls). Hope this helps, Peter From gvasudevan at medarex.com Tue Jul 15 13:32:16 2003 From: gvasudevan at medarex.com (Vasudevan, Geetha) Date: Tue, 15 Jul 2003 10:32:16 -0700 Subject: clustalw question... Message-ID: <8249C3256E593D4FB066BB9998D9F7E41C9B65@ca2-fs03.ca2.2k.medarex.com> Is it possible to force the order of alignment in clustalw? I would like the first seq in the fasta file to be on top. Thanks for your help. -Geetha. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.open-bio.org/pipermail/emboss/attachments/20030715/3d39bd6f/attachment.html From kellert at ohsu.edu Tue Jul 15 13:51:00 2003 From: kellert at ohsu.edu (Thomas Keller) Date: Tue, 15 Jul 2003 10:51:00 -0700 Subject: eprimer3 warning Message-ID: Greetings, Could someone explain the following warning, and give me some advice on what to do about it? % eprimer3 tpn_r01.fa -explain -options Picks PCR primers and hybridization oligos Warning: ajStrFixI called with length 2048 for string with size 2048 .... it repeats this warning about 20 times then proceeds to give options. Thanks, Tom Keller Tom Keller, Ph.D. http://www.ohsu.edu/core kellert at ohsu.edu 503-494-2442 From fernan at iib.unsam.edu.ar Tue Jul 15 14:23:35 2003 From: fernan at iib.unsam.edu.ar (Fernan Aguero) Date: Tue, 15 Jul 2003 15:23:35 -0300 Subject: clustalw question... In-Reply-To: <8249C3256E593D4FB066BB9998D9F7E41C9B66@ca2-fs03.ca2.2k.medarex.com> References: <8249C3256E593D4FB066BB9998D9F7E41C9B66@ca2-fs03.ca2.2k.medarex.com> Message-ID: <20030715182335.GC33270@iib.unsam.edu.ar> +----[ Vasudevan, Geetha (15.Jul.2003 15:09): | | Do you know which option to use? Thanks. Most of the time i run clustalw interactively (i.e. without passing options in the command-line. In this way, I choose option 1 (sequence input), then 2 (MSA), then 9 (output format), then again 9 (toggle output order). The toggle switches between 'aligned' and 'input file'. The last one is the one you want. If you run it non-interactively you need: -OUTORDER= :INPUT or ALIGNED (output from calling 'clustalw -help') Hope this helps, Fernan | | | -----Original Message----- | From: Fernan Aguero [mailto:fernan at iib.unsam.edu.ar] | Sent: Tuesday, July 15, 2003 11:04 AM | To: Vasudevan, Geetha | Subject: Re: clustalw question... | | +----[ Vasudevan, Geetha (15.Jul.2003 14:38): | | | | Is it possible to force the order of alignment in clustalw? I would | | like the first seq in the fasta file to be on top. | | | +----] | | Yes you can. In clustalw, you can set the order of sequences | to be the same of the input file. | | Fernan | | -- | F e r n a n A g u e r o | http://genoma.unsam.edu.ar/~fernan | | +----] -- F e r n a n A g u e r o http://genoma.unsam.edu.ar/~fernan From ableasby at hgmp.mrc.ac.uk Tue Jul 15 14:46:21 2003 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Tue, 15 Jul 2003 19:46:21 +0100 (BST) Subject: eprimer3 warning Message-ID: <200307151846.h6FIkLn19654@bromine.hgmp.mrc.ac.uk> Tom, That message will appear on MacOSX if input files are used which have line lengths >=2048 characters. You need to go to the ftp://ftp.uk.embnet.org/pub/EMBOSS/patchfiles/ directory and get the 'ajsys.c' file (look at the README to see what the other replacement files are for. Just substitute the ajax/ajsys.c file with the new one, recompile/install and the problem should go away. HTH Alan From P.Ernst at dkfz-heidelberg.de Wed Jul 16 04:44:33 2003 From: P.Ernst at dkfz-heidelberg.de (Peter Ernst) Date: Wed, 16 Jul 2003 10:44:33 +0200 (MEST) Subject: acd files In-Reply-To: <3F13D366.2070400@ebi.ac.uk> Message-ID: On Tue, 15 Jul 2003, Peter Rice wrote: > Derek Gatherer wrote: > > So would that allow eg. a Perl script to be called? (I ask because I > > have many old Perl scripts of varying degrees of usefulness, but I am > > now required to provide tools within an EMBOSS-centric department). > > There was also a Perl ACD wrapper from Peter Ernst, and here at EBI we It's the CPAN Bio::Emboss module: http://www.perl.com/CPAN/modules/by-module/Bio/ Usage: for example, a perl version of the EMBOSS program 'seqret', using seqret.acd: --- snip --- use Bio::Emboss qw(:all); embInitPerl("seqret", \@ARGV); $seqall = ajAcdGetSeqall("sequence"); $seqout = ajAcdGetSeqoutall("outseq"); while ($seqall->ajSeqallNext($seq)) { $seqout->ajSeqAllWrite ($seq); } --- snip --- Regards, Peter Ernst -- ======================================================================= Peter Ernst Department of Molecular Biophysics - B020 Deutsches Krebsforschungszentrum (German Cancer Research Center) DKFZ Im Neuenheimer Feld 580 / Technologiepark 3 69120 Heidelberg, Germany phone: +49-6221-42-2330 http://genome.dkfz-heidelberg.de/ fax: +49-6221-42-2333 ======================================================================= From R-4-721447-13602970-2-13541-US2-2A4207A7 at xmr3.com Wed Jul 16 21:31:57 2003 From: R-4-721447-13602970-2-13541-US2-2A4207A7 at xmr3.com (International Scientific Communications, Inc.) Date: Wed, 16 Jul 2003 21:31:57 -0400 Subject: ISC Laboratory Technology News Message-ID: An HTML attachment was scrubbed... URL: http://lists.open-bio.org/pipermail/emboss/attachments/20030716/edc9ad7d/attachment.html From d.gatherer at vir.gla.ac.uk Thu Jul 17 05:53:59 2003 From: d.gatherer at vir.gla.ac.uk (Derek Gatherer) Date: Thu, 17 Jul 2003 10:53:59 +0100 Subject: wrapper for Perl scripts within EMBOSS Message-ID: <5.2.1.1.1.20030717103905.00ad8a60@udcf.gla.ac.uk> Subject: Re: acd files From: Peter Rice (pmr at ebi.ac.uk) Date: Tue 15 Jul 2003 - 11:11:50 BST >time to update the list of EMBOSS wrappers on the web pages >perhaps? I couldn't find this. Is it somewhere in a corner of the website? I have another question, which probably reveals my limited C experience, but anyway... After writing new code, I run 'make', which takes about 3 seconds. But then when I run 'make install', a period of about 7 minutes is consumed by installation of the /share/EMBOSS/data and all the acd files etc, before it gets down to the business of installing the new bin. Is there a way of turning this off, so that 'make install' just jumps to the bare necessary lib and bin installations? acdc is fine after make of course, but that only tests that the acd file is okay. Cheers Derek _________________________ Derek Gatherer Ph.D. Cert.Ed. Computer Officer Institute of Virology Church St. Glasgow G11 5JR Phone: +44 141 330 6268 Fax: +44 141 337 2236 Email: d.gatherer at vir.gla.ac.uk Website: http://www.vir.gla.ac.uk From alfons at elmeuportal.net Thu Jul 17 05:52:42 2003 From: alfons at elmeuportal.net (Alfons Nonell i Canals) Date: 17 Jul 2003 11:52:42 +0200 Subject: A simple question In-Reply-To: <5.2.1.1.1.20030717103905.00ad8a60@udcf.gla.ac.uk> References: <5.2.1.1.1.20030717103905.00ad8a60@udcf.gla.ac.uk> Message-ID: <1058435562.2527.9.camel@anxaneta> Hi! perhaps it is a offtopic question but.. I need help... One friend needs a simple program to run in Linux. She have to edit lots of sequences and, in windows, She is using BioEdit. I ask her to change to Linux but.. She needs this program! Who can tell me about a program BioEdit like for Linux? Thanks. Alfons. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.open-bio.org/pipermail/emboss/attachments/20030717/30b1545b/attachment.html From pmr at ebi.ac.uk Thu Jul 17 05:49:48 2003 From: pmr at ebi.ac.uk (Peter Rice) Date: Thu, 17 Jul 2003 10:49:48 +0100 Subject: wrapper for Perl scripts within EMBOSS References: <5.2.1.1.1.20030717103905.00ad8a60@udcf.gla.ac.uk> Message-ID: <3F16713C.9090107@ebi.ac.uk> Derek Gatherer wrote: > >time to update the list of EMBOSS wrappers on the web pages > >perhaps? > > I couldn't find this. Is it somewhere in a corner of the website? It's linked to the main page as "Jemboss and other Interfaces" > After writing new code, I run 'make', which takes about 3 seconds. But > then when I run 'make install', a period of about 7 minutes is consumed > by installation of the /share/EMBOSS/data and all the acd files etc, > before it gets down to the business of installing the new bin. Is there > a way of turning this off, so that 'make install' just jumps to the bare > necessary lib and bin installations? acdc is fine after make of course, > but that only tests that the acd file is okay. install and libtool have some curious interactions. With shared libraries turned off, I can do: cd emboss make myprogram cp myprogram /where/emboss/binaries/live With shared libraries on, libtool has to run scripts to do the install, and timestamp checking becomes tricky. Hope this helps. No doubt a more authoritative reply from our "make" experts will follow. Peter From gtps5 at gtptech.com Thu Jul 17 05:53:16 2003 From: gtps5 at gtptech.com (Carole Louis) Date: 17 Jul 2003 11:53:16 +0200 Subject: wrapper for Perl scripts within EMBOSS In-Reply-To: <5.2.1.1.1.20030717103905.00ad8a60@udcf.gla.ac.uk> References: <5.2.1.1.1.20030717103905.00ad8a60@udcf.gla.ac.uk> Message-ID: <1058435604.1518.26.camel@thym> Hi, I ask myself the same question :"How to do "make install" quickier ?" . Running this in the repertory "EMBOSS-2.7.1/emboss" this step takes 2 minutes. It's better than 7 minutes but not ideal. Le jeu 17/07/2003 ? 11:53, Derek Gatherer a ?crit : Subject: Re: acd files From: Peter Rice (pmr at ebi.ac.uk) Date: Tue 15 Jul 2003 - 11:11:50 BST >time to update the list of EMBOSS wrappers on the web pages >perhaps? I couldn't find this. Is it somewhere in a corner of the website? I have another question, which probably reveals my limited C experience, but anyway... After writing new code, I run 'make', which takes about 3 seconds. But then when I run 'make install', a period of about 7 minutes is consumed by installation of the /share/EMBOSS/data and all the acd files etc, before it gets down to the business of installing the new bin. Is there a way of turning this off, so that 'make install' just jumps to the bare necessary lib and bin installations? acdc is fine after make of course, but that only tests that the acd file is okay. Cheers Derek _________________________ Derek Gatherer Ph.D. Cert.Ed. Computer Officer Institute of Virology Church St. Glasgow G11 5JR Phone: +44 141 330 6268 Fax: +44 141 337 2236 Email: d.gatherer at vir.gla.ac.uk Website: http://www.vir.gla.ac.uk -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.open-bio.org/pipermail/emboss/attachments/20030717/733fa2b4/attachment.html From gtps5 at gtptech.com Thu Jul 17 06:08:25 2003 From: gtps5 at gtptech.com (Carole Louis) Date: 17 Jul 2003 12:08:25 +0200 Subject: einverted Message-ID: <1058436507.1516.39.camel@thym> Hi (again), I am trying to use the program "einverted" as a function in my own program. "einverted" would be just a part of it. So I have put "einverted" in a function (without all the steps as "embInit", ajAcd....). I have no problem to compile my program but when I try to execute it, my program do not stop. I think the problem is in the lines : for (i = 5 ; i-- ;) { AJCNEW(revmatch[i], (length+maxsave)); ip = revmatch[i]; for(j = length ; j-- ; ) *ip++ = mismatch ; for(j = maxsave ; j-- ;) *ip++ = rogue ; } When I suppress the line "AJCNEW(revmatch[i], (length+maxsave));", the execution of my program do not stop but I obtain a segmentation fault (and it is normal). Is there a special operation to do when I compile ? Thanks, Carole -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.open-bio.org/pipermail/emboss/attachments/20030717/878c603d/attachment.html From inagy at abc.hu Thu Jul 17 06:20:50 2003 From: inagy at abc.hu (Nagy Istvan) Date: Thu, 17 Jul 2003 12:20:50 +0200 Subject: A simple question In-Reply-To: <1058435562.2527.9.camel@anxaneta> References: <5.2.1.1.1.20030717103905.00ad8a60@udcf.gla.ac.uk> <1058435562.2527.9.camel@anxaneta> Message-ID: <20030717122050.4bb8f9ff.inagy@abc.hu> On 17 Jul 2003 11:52:42 +0200 Alfons Nonell i Canals wrote: > Who can tell me about a program BioEdit like for Linux? Besides EMBOSS and the Staden package I use GDE on Linux. GDE is nice and flexible and the best for sequence editing. Unfortunatelly it is a little bit old-fashioned and configuring it some investment of time and dedication. From d.gatherer at vir.gla.ac.uk Thu Jul 17 07:01:08 2003 From: d.gatherer at vir.gla.ac.uk (Derek Gatherer) Date: Thu, 17 Jul 2003 12:01:08 +0100 Subject: wrapper for Perl scripts within EMBOSS In-Reply-To: <3F16713C.9090107@ebi.ac.uk> References: <5.2.1.1.1.20030717103905.00ad8a60@udcf.gla.ac.uk> Message-ID: <5.2.1.1.1.20030717115926.00aaf040@udcf.gla.ac.uk> >With shared libraries turned off, I can do: Yes, this does the trick, thanks. ./configure --disable-shared just needs to be run once. Cheers Derek From mad at biol.unlp.edu.ar Thu Jul 17 08:08:39 2003 From: mad at biol.unlp.edu.ar (=?ISO-8859-1?Q?Mart=EDn_Sarachu?=) Date: Thu, 17 Jul 2003 09:08:39 -0300 Subject: EMBOSS programming course Message-ID: <3F1691C7.80804@biol.unlp.edu.ar> Hi list, anybody in here is going to the EMBOSS programming course on September? Regards, martin -- Mart?n Sarachu mad at biol.unlp.edu.ar EMBNet Argentina http://www.ar.embnet.org From d.gatherer at vir.gla.ac.uk Thu Jul 17 08:30:17 2003 From: d.gatherer at vir.gla.ac.uk (Derek Gatherer) Date: Thu, 17 Jul 2003 13:30:17 +0100 Subject: wrapper for Perl scripts within EMBOSS In-Reply-To: <3F16713C.9090107@ebi.ac.uk> References: <5.2.1.1.1.20030717103905.00ad8a60@udcf.gla.ac.uk> Message-ID: <5.2.1.1.1.20030717131011.00ac0008@udcf.gla.ac.uk> So the following would presumably be the simplest possible wrapper, just opening and running a Perl script, using a single line ACD file just to name the program and nothing else. However, the Perl script then needs to prompt for any further parameters, infiles etc. This works, but is it against the EMBOSS philosophy? I did try collecting the Perl parameters via the ACD, but didn't manage to figure out a way of easily manipulating them into the command line (ie. ajSystemEnv( &cmd, env) ). I tried things like strcat(str1, str 2) and so on, but kept running into type incompatibilities with AjPStr. Is there a standard way to push the usual collected strings from the ACD file into a concatenated string that can then act as the @ARGV for a Perl script and be called via ajSystemEnv( &cmd, env) etc? #--------------ACD file, hello.acd--------------------------------------# appl: hello [ doc: "Calls a Perl script which then does the rest of what you want to do" ] #--------------hello.c wrapper to call hello.pl-----------------------# #include "emboss.h" int main(int argc, char **argv, char **env) { AjPStr cmd=NULL; char *prog_default = "perl -w path/to/bin/hello.pl"; embInit("hello",argc,argv); // invoke the command if (!ajNamGetValueC("perl -w path/to/bin/hello.pl", &cmd)) cmd = ajStrNewC(prog_default); ajFmtError( "..%s..\n\n", ajStrStr( cmd)); ajDebug( "Executing '%S'\n", cmd); ajSystemEnv( &cmd, env); ajExit(); return 0; } From P.Ernst at dkfz-heidelberg.de Thu Jul 17 10:27:27 2003 From: P.Ernst at dkfz-heidelberg.de (Peter Ernst) Date: Thu, 17 Jul 2003 16:27:27 +0200 (MEST) Subject: wrapper for Perl scripts within EMBOSS In-Reply-To: <5.2.1.1.1.20030717131011.00ac0008@udcf.gla.ac.uk> Message-ID: On Thu, 17 Jul 2003, Derek Gatherer wrote: > So the following would presumably be the simplest possible wrapper, just > opening and running a Perl script, using a single line ACD file just to > name the program and nothing else. I think I am missing the point in this strategy. What is the advantage of having a C-Emboss wrapper around a Perl program, if you do not use any of the ACD features (eg. reading sequences)? Also, something like "-help" on the command-line will lead embInit() to dump senseless information. > However, the Perl script then needs to prompt for any further > parameters, infiles etc. Yes, because embInit() doesn't know about it. > This works, but is it against the EMBOSS philosophy? I did try > collecting the Perl parameters via the ACD, but didn't manage to > figure out a way of easily manipulating them into the command line > (ie. ajSystemEnv( &cmd, env) ). The question is here what you really want? If you don't want Emboss/ACD to interfere with your command-line, you better avoid calling embInit(). :-) However, if you want ACD to do some part of the job for you, then one has to define, what part of the work you want to leave for ACD, and what you want to do yourself in your Perl program. An example: If one of the input parameters is supposed to be an input sequence, what do you want to have? 1. The sequence as string (in what format)? 2. The filename (what to do with DB entries?) ? What to do with defaults evaluated by ACD? In fact I see 2 strategies: A.) ignore ACD B.) use ACD to work on the command-line, read in sequences, do prompting, etc... But then you have the problem to access the information ACD has collected. For exactly this purpose, there are the set of ajAcdGet....() functions in Emboss. Here is an example, how to use these functions in Perl to get the input sequence as a Perl-string from ACD: test1.acd: ---------- appl: test1 [ doc: "test1 Perl script" ] sequence: sequence [ param: "Y" req: "Y" ] test1.pl: --------- #!/usr/bin/perl # --- import all EMBOSS functions into this namespace use Bio::Emboss qw(:all); # --- store script and acd file in the same directory ($thisdir = $0) =~ s:[^/]*$::; $thisdir = "." unless length ($thisdir); $ENV{"EMBOSS_ACDROOT"} = $thisdir; embInitPerl("test1", \@ARGV); my $seqstr = ajAcdGetSeq("sequence")->ajSeqChar(); print $seqstr; usage: ------ % perl test1.pl swissprot:edd_rat test1 Perl script ARRERMTAREEASLRTLEGRRRATLLSARQGMMSARGDFLNYALSLMRSHNDEHSDVLPVLDVCSLK... or % perl test1.pl test1 Perl script Input sequence: swissprot:edd_rat ARRERMTAREEASLRTLEGRRRATLLSARQGMMSARGDFLNYALSLMRSHNDEHSDVLPVL.... and % perl test1.pl -help Mandatory qualifiers: [-sequence] sequence (no help text) sequence value Optional qualifiers: (none) Advanced qualifiers: (none) General qualifiers: -help boolean Report command line options. More information on associated and general qualifiers can be found with -help -verbose Kind regards, Peter Ernst -- ======================================================================= Peter Ernst Department of Molecular Biophysics - B020 Deutsches Krebsforschungszentrum (German Cancer Research Center) DKFZ Im Neuenheimer Feld 580 / Technologiepark 3 69120 Heidelberg, Germany phone: +49-6221-42-2330 http://genome.dkfz-heidelberg.de/ fax: +49-6221-42-2333 ======================================================================= > > #--------------ACD file, hello.acd--------------------------------------# > > appl: hello [ > doc: "Calls a Perl script which then does the rest of what you > want to do" > ] > > #--------------hello.c wrapper to call hello.pl-----------------------# > > #include "emboss.h" > > int main(int argc, char **argv, char **env) > { > AjPStr cmd=NULL; > > char *prog_default = "perl -w path/to/bin/hello.pl"; > > embInit("hello",argc,argv); > > // invoke the command > > if (!ajNamGetValueC("perl -w path/to/bin/hello.pl", &cmd)) > cmd = ajStrNewC(prog_default); > > ajFmtError( "..%s..\n\n", ajStrStr( cmd)); > ajDebug( "Executing '%S'\n", cmd); > ajSystemEnv( &cmd, env); > > ajExit(); > > return 0; > } From pmr at ebi.ac.uk Thu Jul 17 10:38:10 2003 From: pmr at ebi.ac.uk (Peter Rice) Date: Thu, 17 Jul 2003 15:38:10 +0100 Subject: wrapper for Perl scripts within EMBOSS References: Message-ID: <3F16B4D2.7020903@ebi.ac.uk> Peter Ernst wrote: > I think I am missing the point in this strategy. > > What is the advantage of having a C-Emboss wrapper around a Perl > program, if you do not use any of the ACD features (eg. reading > sequences)? It depends on how you run it. In Martin Senger's SoapLab interface, third party applications (including perl scripts) are defined by ACD files. These are used to automatically define the SOAP interface, and SoapLab handles conversion of the sequence types into something the third party application can use (Martin defines special "comment" attributes in his ACD files for this). But ... in SoapLab ACD is only used to define the interface ... SoapLab and the third party applications do not read the ACD file at run time. It would be fun, though, to be able to use ACD directly in perl. Hmmm ... I wonder ... Peter From maoj at mail.nih.gov Thu Jul 17 10:41:25 2003 From: maoj at mail.nih.gov (Jean Mao) Date: Thu, 17 Jul 2003 10:41:25 -0400 Subject: question about emboss logging Message-ID: <002201c34c71$80014c50$494de780@CIT.NIH.GOV> Hi, the default logging info contains 3 fields: program user time/date Is there a way to modify the logging system so that other info can be recorded such as CPU time, machine name etc.? Thanks. Jean -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.open-bio.org/pipermail/emboss/attachments/20030717/78e0024a/attachment.html From pmr at ebi.ac.uk Thu Jul 17 10:43:00 2003 From: pmr at ebi.ac.uk (Peter Rice) Date: Thu, 17 Jul 2003 15:43:00 +0100 Subject: question about emboss logging References: <002201c34c71$80014c50$494de780@CIT.NIH.GOV> Message-ID: <3F16B5F4.6010602@ebi.ac.uk> Jean Mao wrote: > Hi, the default logging info contains 3 fields: program user time/date > > Is there a way to modify the logging system so that other info can be > recorded such as CPU time, machine name etc.? Thanks. It is easy to do ... Would it be useful? What information would you like? For example, we can put a header on the first record of the log file to say what information is required in each column, and log that way. Or we could make the logfile syntax more complicated - but we do not try to lock the file so there may be a few merged records in a very large file. For statistics they are not a problem. Peter From P.Ernst at dkfz-heidelberg.de Thu Jul 17 11:00:16 2003 From: P.Ernst at dkfz-heidelberg.de (Peter Ernst) Date: Thu, 17 Jul 2003 17:00:16 +0200 (MEST) Subject: wrapper for Perl scripts within EMBOSS In-Reply-To: <3F16B4D2.7020903@ebi.ac.uk> Message-ID: On Thu, 17 Jul 2003, Peter Rice wrote: > In Martin Senger's SoapLab interface, third party applications > (including perl scripts) are defined by ACD files. I think we must distinguish between the "ACD language" and the "ACD code in Emboss". Several interfaces to Emboss read files in the ACD language to build the interface to Emboss programs. However most (all?, what about Jemboss?) interfaces do not use the ACD code in Emboss to actually perform the reading. > But ... in SoapLab ACD is only used to define the interface ... SoapLab > and the third party applications do not read the ACD file at run time. > > It would be fun, though, to be able to use ACD directly in perl. This is what Perl Bio::Emboss is doing. Calling embInit() from libajax and embInit() performs all the ACD processing. Bio::Emboss just translates Perl syntax into calls to the libajax functions and back-translates some of the C data-types into Perl types. Peter Ernst From tcarver at hgmp.mrc.ac.uk Thu Jul 17 11:07:55 2003 From: tcarver at hgmp.mrc.ac.uk (Dr T. Carver) Date: Thu, 17 Jul 2003 16:07:55 +0100 (BST) Subject: wrapper for Perl scripts within EMBOSS In-Reply-To: Message-ID: > Several interfaces to Emboss read files in the ACD language to build > the interface to Emboss programs. However most (all?, what about > Jemboss?) interfaces do not use the ACD code in Emboss to actually > perform the reading. Jemboss parses the ACD files to produce the forms and calculate any inter-dependencies between parameters. From this is simply construct the command line. Tim From bgibbon at email.arizona.edu Thu Jul 17 13:10:47 2003 From: bgibbon at email.arizona.edu (Bryan Gibbon) Date: Thu, 17 Jul 2003 10:10:47 -0700 Subject: Problems compiling on MacOS X Message-ID: Hello, I am having trouble getting any recent version of EMBOSS to compile on MacOS X.2.6 (no problem for me on redhat). I am using the Dec 2002 developer tools package. I have also tried downloading and installing the most recent versions of GNU make and m4 as suggested on the EMBOSS website. The error occurs when the ajax libraries begin to be compiled but I am not familiar enough with configure/make/gcc to figure out what is going on. Below are the commands that I used to try building after the make and m4 installation and the output just prior to the error: make distclean ./configure make Making all in ajax source='ajacd.c' object='ajacd.lo' libtool=yes \ depfile='.deps/ajacd.Plo' tmpdepfile='.deps/ajacd.TPlo' \ depmode=gcc /bin/sh ../depcomp \ /bin/sh ../libtool --mode=compile gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACK AGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"EMBOSS\" -DVERSION=\"2. 7.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLI B_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES _H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DX_DISPLAY_MISSING=1 -DHAVE_DIRENT _H=1 -DSTDC_HEADERS=1 -DHAVE_UNISTD_H=1 -DGETPGRP_VOID=1 -DHAVE_STRFTIME=1 - DHAVE_UNISTD_H=1 -DHAVE_FORK=1 -DHAVE_VFORK=1 -DHAVE_WORKING_VFORK=1 -DHAVE_ WORKING_FORK=1 -DHAVE_VPRINTF=1 -DHAVE_MEMMOVE=1 -DHAVE_LIBM=1 -I. -I. -DAJ AX_FIXED_ROOT=\"/Users/bgibbon/source code/EMBOSS-2.7.1/emboss\" -DPREFIX=\"/usr/local\" -I../plplot -DNO_AUTH - g -O2 -c -o ajacd.lo `test -f 'ajacd.c' || echo './'`ajacd.c mkdir .libs gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACK AGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"EMBOSS\" -DVERSION=\"2. 7.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLI B_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES _H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DX_DISPLAY_MISSING=1 -DHAVE_DIRENT _H=1 -DSTDC_HEADERS=1 -DHAVE_UNISTD_H=1 -DGETPGRP_VOID=1 -DHAVE_STRFTIME=1 - DHAVE_UNISTD_H=1 -DHAVE_FORK=1 -DHAVE_VFORK=1 -DHAVE_WORKING_VFORK=1 -DHAVE_ WORKING_FORK=1 -DHAVE_VPRINTF=1 -DHAVE_MEMMOVE=1 -DHAVE_LIBM=1 -I. -I. -DAJA X_FIXED_ROOT=\"/Users/bgibbon/source code/EMBOSS-2.7.1/emboss\" -DPREFIX=\"/usr/local\" -I../plplot -DNO_AUTH -g -O2 -c ajacd.c -Wp,-MD,.deps/ajacd.TPlo -fno-common -DPIC -o .libs/ajacd.o gcc: cannot specify -o with -c or -S and multiple compilations make[1]: *** [ajacd.lo] Error 1 make: *** [all-recursive] Error 1 Bryan Gibbon Department of Plant Sciences University of Arizona Tucson, AZ 85721 Phone- 520-621-9154 Fax- 520-621-3692 http://ag.arizona.edu/research/larkinslab/members/gibbon.htm From kvddrift at earthlink.net Thu Jul 17 17:51:18 2003 From: kvddrift at earthlink.net (Koen van der Drift) Date: Thu, 17 Jul 2003 17:51:18 -0400 Subject: Problems compiling on MacOS X In-Reply-To: Message-ID: On Thursday, July 17, 2003, at 01:10 PM, Bryan Gibbon wrote: > Hello, > I am having trouble getting any recent version of EMBOSS to compile on > MacOS > X.2.6 (no problem for me on redhat). I am using the Dec 2002 developer > tools > package. I have also tried downloading and installing the most recent > versions of GNU make and m4 as suggested on the EMBOSS website. Bryan, Try installing EMBOSS through the fink system (fink.sf.net). After installing fink, just type 'fink install emboss'. This will take care of downloading, compiling, and installing all necessary packages. Note that from a fresh fink EMBOSS 2.6.0 will be installed. Version 2.7.1 is available, but only as a so-called 'unstable' package. See the fink docs how to enable the unstable packages. After that, again type 'fink install emboss'. Good luck, - Koen. From kellert at ohsu.edu Thu Jul 17 18:11:04 2003 From: kellert at ohsu.edu (Thomas Keller) Date: Thu, 17 Jul 2003 15:11:04 -0700 Subject: Problems compiling on MacOS X In-Reply-To: Message-ID: <8E843979-B8A3-11D7-86E5-0003930405E2@ohsu.edu> Bill Van Etten at the BioTeam has put together some installers for Mac OS X. He's down one for emboss-2.5.1. I've used them and they've worked well. You can download from http://bioteam.net/MacOSX/biotools-1/ Good luck, Tom Keller On Thursday, July 17, 2003, at 10:10 AM, Bryan Gibbon wrote: > Hello, > I am having trouble getting any recent version of EMBOSS to compile on > MacOS > X.2.6 (no problem for me on redhat). I am using the Dec 2002 developer > tools > package. I have also tried downloading and installing the most recent > versions of GNU make and m4 as suggested on the EMBOSS website. The > error > occurs when the ajax libraries begin to be compiled but I am not > familiar > enough with configure/make/gcc to figure out what is going on. Below > are the > commands that I used to try building after the make and m4 > installation and > the output just prior to the error: > > make distclean > ./configure > make > > Making all in ajax > source='ajacd.c' object='ajacd.lo' libtool=yes \ > depfile='.deps/ajacd.Plo' tmpdepfile='.deps/ajacd.TPlo' \ > depmode=gcc /bin/sh ../depcomp \ > /bin/sh ../libtool --mode=compile > gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" > -DPACK > AGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"EMBOSS\" > -DVERSION=\"2. > 7.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 > -DHAVE_STDLI > B_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 > -DHAVE_INTTYPES > _H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DX_DISPLAY_MISSING=1 > -DHAVE_DIRENT > _H=1 -DSTDC_HEADERS=1 -DHAVE_UNISTD_H=1 -DGETPGRP_VOID=1 > -DHAVE_STRFTIME=1 - > DHAVE_UNISTD_H=1 -DHAVE_FORK=1 -DHAVE_VFORK=1 -DHAVE_WORKING_VFORK=1 > -DHAVE_ > WORKING_FORK=1 -DHAVE_VPRINTF=1 -DHAVE_MEMMOVE=1 -DHAVE_LIBM=1 -I. > -I. -DAJ > AX_FIXED_ROOT=\"/Users/bgibbon/source > code/EMBOSS-2.7.1/emboss\" -DPREFIX=\"/usr/local\" -I../plplot > -DNO_AUTH - > g -O2 -c -o ajacd.lo `test -f 'ajacd.c' || echo './'`ajacd.c > mkdir .libs > > gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" > -DPACK > AGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"EMBOSS\" > -DVERSION=\"2. > 7.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 > -DHAVE_STDLI > B_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 > -DHAVE_INTTYPES > _H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DX_DISPLAY_MISSING=1 > -DHAVE_DIRENT > _H=1 -DSTDC_HEADERS=1 -DHAVE_UNISTD_H=1 -DGETPGRP_VOID=1 > -DHAVE_STRFTIME=1 - > DHAVE_UNISTD_H=1 -DHAVE_FORK=1 -DHAVE_VFORK=1 -DHAVE_WORKING_VFORK=1 > -DHAVE_ > WORKING_FORK=1 -DHAVE_VPRINTF=1 -DHAVE_MEMMOVE=1 -DHAVE_LIBM=1 -I. -I. > -DAJA > X_FIXED_ROOT=\"/Users/bgibbon/source > code/EMBOSS-2.7.1/emboss\" -DPREFIX=\"/usr/local\" -I../plplot > -DNO_AUTH -g > -O2 -c ajacd.c -Wp,-MD,.deps/ajacd.TPlo -fno-common -DPIC -o > .libs/ajacd.o > gcc: cannot specify -o with -c or -S and multiple compilations > make[1]: *** [ajacd.lo] Error 1 > make: *** [all-recursive] Error 1 > > Bryan Gibbon > Department of Plant Sciences > University of Arizona > Tucson, AZ 85721 > > Phone- 520-621-9154 > Fax- 520-621-3692 > > http://ag.arizona.edu/research/larkinslab/members/gibbon.htm > > From mbb8n at virginia.edu Thu Jul 17 20:34:46 2003 From: mbb8n at virginia.edu (Michael Black) Date: Thu, 17 Jul 2003 20:34:46 -0400 Subject: Problems compiling on MacOS X Message-ID: <7538FDE0-B8BF-11D7-95E4-0003931D9E4A@virginia.edu> Sorry I can't offer any specific answer, and I have read the responses you've received. I can say that I have installed EMBOSS 2.7.1 on two Apple OS X machines without any problems. These were a TiBook and DP 1.25 PowerMac, both running 10.2.6, with the Dec. 2002 developers tools, but with the gcc 3.3 patch applied. The libajax installed fine. I do not like installing EMBOSS via FINK (which I do use for other installs), since I want the control of a stand alone install (in /usr/local/bin, with png support), and I use the standalone version of JemBoss (which also installed fine). All I can suggest is manually removing any previous EMBOSS libs, and trying the install again - from my experience it should work flawlessly, but I did completely blow away my previous 2.6.0 installs before installing 2.7.1. Oh, and I did use FINK to install libpng and gd, but that has worked fine for me since at least EMBOSS 2.5 Best of luck, Michael ____________________________________________ Michael B. Black, Ph.D. Molecular Biology Computing Support ITC-ACHS, Univ. of Virginia ____________________________________________ On Thursday, July 17, 2003, at 01:10 PM, Bryan Gibbon wrote: > Hello, > I am having trouble getting any recent version of EMBOSS to compile on > MacOS > X.2.6 (no problem for me on redhat). I am using the Dec 2002 developer > tools > package. I have also tried downloading and installing the most recent > versions of GNU make and m4 as suggested on the EMBOSS website. The > error > occurs when the ajax libraries begin to be compiled but I am not > familiar > enough with configure/make/gcc to figure out what is going on. Below > are the > commands that I used to try building after the make and m4 > installation and > the output just prior to the error: > > make distclean > ./configure > make > > Making all in ajax > source='ajacd.c' object='ajacd.lo' libtool=yes \ > depfile='.deps/ajacd.Plo' tmpdepfile='.deps/ajacd.TPlo' \ > depmode=gcc /bin/sh ../depcomp \ > /bin/sh ../libtool --mode=compile > gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" > -DPACK > AGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"EMBOSS\" > -DVERSION=\"2. > 7.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 > -DHAVE_STDLI > B_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 > -DHAVE_INTTYPES > _H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DX_DISPLAY_MISSING=1 > -DHAVE_DIRENT > _H=1 -DSTDC_HEADERS=1 -DHAVE_UNISTD_H=1 -DGETPGRP_VOID=1 > -DHAVE_STRFTIME=1 - > DHAVE_UNISTD_H=1 -DHAVE_FORK=1 -DHAVE_VFORK=1 -DHAVE_WORKING_VFORK=1 > -DHAVE_ > WORKING_FORK=1 -DHAVE_VPRINTF=1 -DHAVE_MEMMOVE=1 -DHAVE_LIBM=1 -I. > -I. -DAJ > AX_FIXED_ROOT=\"/Users/bgibbon/source > code/EMBOSS-2.7.1/emboss\" -DPREFIX=\"/usr/local\" -I../plplot > -DNO_AUTH - > g -O2 -c -o ajacd.lo `test -f 'ajacd.c' || echo './'`ajacd.c > mkdir .libs > > gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" > -DPACK > AGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"EMBOSS\" > -DVERSION=\"2. > 7.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 > -DHAVE_STDLI > B_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 > -DHAVE_INTTYPES > _H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DX_DISPLAY_MISSING=1 > -DHAVE_DIRENT > _H=1 -DSTDC_HEADERS=1 -DHAVE_UNISTD_H=1 -DGETPGRP_VOID=1 > -DHAVE_STRFTIME=1 - > DHAVE_UNISTD_H=1 -DHAVE_FORK=1 -DHAVE_VFORK=1 -DHAVE_WORKING_VFORK=1 > -DHAVE_ > WORKING_FORK=1 -DHAVE_VPRINTF=1 -DHAVE_MEMMOVE=1 -DHAVE_LIBM=1 -I. -I. > -DAJA > X_FIXED_ROOT=\"/Users/bgibbon/source > code/EMBOSS-2.7.1/emboss\" -DPREFIX=\"/usr/local\" -I../plplot > -DNO_AUTH -g > -O2 -c ajacd.c -Wp,-MD,.deps/ajacd.TPlo -fno-common -DPIC -o > .libs/ajacd.o > gcc: cannot specify -o with -c or -S and multiple compilations > make[1]: *** [ajacd.lo] Error 1 > make: *** [all-recursive] Error 1 > > Bryan Gibbon > Department of Plant Sciences > University of Arizona > Tucson, AZ 85721 > > Phone- 520-621-9154 > Fax- 520-621-3692 > > http://ag.arizona.edu/research/larkinslab/members/gibbon.htm > > From d.gatherer at vir.gla.ac.uk Fri Jul 18 04:42:38 2003 From: d.gatherer at vir.gla.ac.uk (Derek Gatherer) Date: Fri, 18 Jul 2003 09:42:38 +0100 Subject: wrapper for Perl scripts within EMBOSS In-Reply-To: References: <5.2.1.1.1.20030717131011.00ac0008@udcf.gla.ac.uk> Message-ID: <5.2.1.1.1.20030718093617.00a9bcc8@udcf.gla.ac.uk> At 16:27 17/07/2003 +0200, Peter Ernst wrote: > use Bio::Emboss qw(:all); Yes, thanks, this appears to be what I'm looking for. Just for clarification, Bio::EMBOSS http://search.cpan.org/author/PERNST/Bio-Emboss-0.3/Emboss.pm does not require BioPerl, unlike Bio::Factory::EMBOSS http://doc.bioperl.org/releases/bioperl-1.2/Bio/Factory/EMBOSS.html ??? Cheers Derek From bgibbon at email.arizona.edu Sun Jul 20 12:40:35 2003 From: bgibbon at email.arizona.edu (Bryan Gibbon) Date: Sun, 20 Jul 2003 09:40:35 -0700 Subject: Problems compiling on MacOS X In-Reply-To: Message-ID: Hello, Thanks for the prompt responses to my question. It turns out that the problem was with either the capital "S" or the space in by directory named "Source code". EMBOSS built without a problem when I changed the directory name to "src". I need to remember to stick to Unix conventions when working at the command line in OS X! Bryan Gibbon From Peter.Robinson at t-online.de Sun Jul 20 15:16:12 2003 From: Peter.Robinson at t-online.de (peter robinson) Date: Sun, 20 Jul 2003 21:16:12 +0200 Subject: vector vs AjPInt2D Message-ID: <200307202116.12103.peter.robinson@t-online.de> Dear EMBOSSers, from perusal of SRS I take it that AjPInt2D is intended to be something like C++'s vector. I would like to use this for a new CpG program in order to store locations of C, G, CG in order to avoid repeatedly scanning the input sequence (I will probably try some sort of buffer to avoid blowing up the space requirements too much). I was wondering if anyone could point me to a good example of using AjPInt2D for this purpose? Thanks Peter From f.jossinet at ibmc.u-strasbg.fr Mon Jul 21 06:09:13 2003 From: f.jossinet at ibmc.u-strasbg.fr (Fabrice Jossinet) Date: Mon, 21 Jul 2003 12:09:13 +0200 Subject: take care about GU pairs in RNA sequences Message-ID: <200307211209.13666.f.jossinet@ibmc.u-strasbg.fr> Hi all, EMBOSS applications are very nice for nucleotides sequences analyses. But if the sequence is an RNA one, allowing GU/GT base pairs is not an available option. Does somebody try something to resolve that ? Thank you, Fabrice J -- ------------------------------------------------------------------------ Dr. Fabrice Jossinet Institut de biologie moleculaire et cellulaire, UPR9002, CNRS Universite Louis Pasteur 15 rue Rene Descartes F-67084 Strasbourg Cedex France Tel + 33 (0) 3 88 417044 FAX + 33 (0) 3 88 417066 or + 33 (0) 3 60 22 18 (long faxes) f.jossinet at ibmc.u-strasbg.fr http://www.fjossi.net/ http://www-ibmc.u-strasbg.fr/upr9002/westhof/ ------------------------------------------------------------------------ From rcalma at mondenet.com Tue Jul 22 16:06:16 2003 From: rcalma at mondenet.com (Canada Books) Date: Tue, 22 Jul 2003 16:06:16 -0400 Subject: Federal provincial funds Message-ID: <20030722200529.41F857D21F@mercury.hgmp.mrc.ac.uk> CANADA BOOKS 36 Felix Renaud Aylmer Qc J9H 7C1 (819)682-7983 PRESS RELEASE CANADIAN SUBSIDY DIRECTORY YEAR 2003 EDITION Legal Deposit-National Library of Canada ISBN 2-922870-05-7 The new revised edition of the Canadian Subsidy Directory 2003 is now available. The new edition is the most complete and affordable reference for anyone looking for financial support. It is deemed to be the perfect tool for new or existing businesses, individual ventures, foundations and associations. This Publication contains more than 2000 direct and indirect financial subsidies, grants and loans offered by government departments and agencies, foundations, associations and organisations. In this new 2003 edition all programs are well described. The Canadian Subsidy Directory is the most comprehensive tool to start up a business, improve existent activities, set up a business plan, or obtain assistance from experts in fields such as: Industry, transport, agriculture, communications, municipal infrastructure, education, import-export, labor, construction and renovation, the service sector, hi-tech industries, research and development, joint ventures, arts, cinema, theatre, music and recording industry, the self employed, contests, and new talents. Assistance from and for foundations and associations, guidance to prepare a business plan, market surveys, computers, and much more! The Canadian Subsidy Directory is sold $ 69.95, to obtain a copy please call: Canada Books, (819)682-7983 or Canadian business resource center (250)381-4822 From yoskim at NMSU.Edu Wed Jul 23 18:17:49 2003 From: yoskim at NMSU.Edu (Yosep) Date: Wed, 23 Jul 2003 16:17:49 -0600 (MDT) Subject: Runtime error... Message-ID: Hello! I have finally & succesfully instally Jemboss on my NetBSD machine, meaning I didn't get any installing error. Now, I followed the online help for setting up the environment variables and so on for the Standalone Mode. However, I get this error message when I run the "runJemboss.csh" script. yosep at typha: {599} ./runJemboss.csh [1] 6526 yosep at typha: {600} Standalone mode Font specified in font.properties not found [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] Font specified in font.properties not found [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] Font specified in font.properties not found [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] Font specified in font.properties not found [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] Font specified in font.properties not found [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] Font specified in font.properties not found [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] Font specified in font.properties not found [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] Font specified in font.properties not found [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] Font specified in font.properties not found [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] Font specified in font.properties not found [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] Font specified in font.properties not found [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] Font specified in font.properties not found [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] Font specified in font.properties not found [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] Font specified in font.properties not found [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] Font specified in font.properties not found [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] Font specified in font.properties not found [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] Font specified in font.properties not found [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] Font specified in font.properties not found [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] Font specified in font.properties not found [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] Font specified in font.properties not found [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] /packages/emboss/STABLE/bin/wossname -colon -auto RunEmbossApplication Error executing: /packages/emboss/STABLE/bin/wossname -colon -auto java.lang.NullPointerException at org.emboss.jemboss.programs.RunEmbossApplication.isProcessStdout(RunEmbossApplication.java:71) at org.emboss.jemboss.gui.BuildProgramMenu$1.construct(BuildProgramMenu.java:231) at org.emboss.jemboss.gui.SwingWorker$2.run(SwingWorker.java:127) at java.lang.Thread.run(Thread.java:479) How can I fix these errors? Any help would be greatly appreciated. ============= |\/\/| | Yosep Kim |,,,,| | NMSU Computer Lab Assistant | | | Computer Science, B.S. [|^ ^|] | New Mexico State Unversity \__/ | http://web.nmsu.edu/~yoskim ============= PHIL 4:13 From tcarver at hgmp.mrc.ac.uk Thu Jul 24 02:11:46 2003 From: tcarver at hgmp.mrc.ac.uk (Dr T. Carver) Date: Thu, 24 Jul 2003 07:11:46 +0100 (BST) Subject: Runtime error... In-Reply-To: Message-ID: Hi Yosep These errors look like you may not have used the install script provided (EMBOSS-2.7.1/jemboss/utils/install-jemboss-server.sh) with a fresh download of EMBOSS-2.7.1. This should have changed the values in $EMBOSS_INSTALL/share/EMBOSS/jemboss/resources/jemboss.properties to reflect the directory structure for your installation. If you did not use the install script, I recommend you try using that. If you did then you can try editing: $EMBOSS_INSTALL/share/EMBOSS/jemboss/resources/jemboss.properties and look at the description of the variables at: http://www.hgmp.mrc.ac.uk/Software/EMBOSS/Jemboss/install/properties.html Hope this helps. Regards Tim Carver HGMP-RC On Wed, 23 Jul 2003, Yosep wrote: > > Hello! > > I have finally & succesfully instally Jemboss on my NetBSD machine, > meaning I didn't get any installing error. Now, I followed the online > help for setting up the environment variables and so on for the Standalone > Mode. However, I get this error message when I run the "runJemboss.csh" > script. > > yosep at typha: {599} ./runJemboss.csh > [1] 6526 > yosep at typha: {600} Standalone mode > Font specified in font.properties not found > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] > Font specified in font.properties not found > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] > Font specified in font.properties not found > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] > Font specified in font.properties not found > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] > Font specified in font.properties not found > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] > Font specified in font.properties not found > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] > Font specified in font.properties not found > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] > Font specified in font.properties not found > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] > Font specified in font.properties not found > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] > Font specified in font.properties not found > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] > Font specified in font.properties not found > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] > Font specified in font.properties not found > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] > Font specified in font.properties not found > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] > Font specified in font.properties not found > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] > Font specified in font.properties not found > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] > Font specified in font.properties not found > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] > Font specified in font.properties not found > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] > Font specified in font.properties not found > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] > Font specified in font.properties not found > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] > Font specified in font.properties not found > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] > /packages/emboss/STABLE/bin/wossname -colon -auto > RunEmbossApplication Error executing: /packages/emboss/STABLE/bin/wossname -colon -auto > java.lang.NullPointerException > at org.emboss.jemboss.programs.RunEmbossApplication.isProcessStdout(RunEmbossApplication.java:71) > at org.emboss.jemboss.gui.BuildProgramMenu$1.construct(BuildProgramMenu.java:231) > at org.emboss.jemboss.gui.SwingWorker$2.run(SwingWorker.java:127) > at java.lang.Thread.run(Thread.java:479) > > How can I fix these errors? > Any help would be greatly appreciated. > > > ============= > |\/\/| | Yosep Kim > |,,,,| | NMSU Computer Lab Assistant > | | | Computer Science, B.S. > [|^ ^|] | New Mexico State Unversity > \__/ | http://web.nmsu.edu/~yoskim > ============= > PHIL 4:13 > From gwilliam at hgmp.mrc.ac.uk Thu Jul 24 10:55:40 2003 From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522) Date: Thu, 24 Jul 2003 15:55:40 +0100 Subject: Do you have an interface to EMBOSS? Message-ID: <3F1FF36C.CE33B7E5@hgmp.mrc.ac.uk> We would like to update our web page http://www.hgmp.mrc.ac.uk/Software/EMBOSS/interfaces.html describing the details of interfaces that people have developed for EMBOSS. If you have an interface that is not described on this page, or if you have an interface that could be described better, please reply to me or this mailing list. Many thanks, Gary -- Gary Williams Tel: +44 1223 494522 Fax: +44 1223 494512 mailto:G.Williams at hgmp.mrc.ac.uk http://www.hgmp.mrc.ac.uk/ Bioinformatics, MRC HGMP, Hinxton, Cambridge, CB10 1SB, UK From alfons at elmeuportal.net Fri Jul 25 06:24:08 2003 From: alfons at elmeuportal.net (Alfons Nonell i Canals) Date: 25 Jul 2003 12:24:08 +0200 Subject: Consed users. Message-ID: <1059128648.2521.30.camel@anxaneta> Hi! I know that is, perhaps, an oftopic message but,I need help and some of you can told me how to resolve a little problem. I'm a young student that is using phred-phra-consed to assembly lots of seq?ences. One day, when I added new reads to my assembly, in the bash terminal appeared an error like it: 1: Can't figure out read type for 1_S2APIII_A02_S2APIII_1.b.ab1.phd.1 since after the underscore is S2APIII_A02_S2APIII_1 1: Can't figure out read type for 1_S2APIII_A03_S2APIII_1.b.ab1.phd.1 since after the underscore is S2APIII_A03_S2APIII_1 After that, I updated my consed (v12) to the latest version, 13 but... the problem didn't disapear... I've studiet all perl scripts of the package and I've discovered a line in determineReadtypes.perl with that errror but.. I don't know the meaning of it. Somebody can help me? I need that programs to my job research... Thanks. Alfons. Departament de Gen?tica i microbiologia. Universitat Aut?noma de Barcelona -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.open-bio.org/pipermail/emboss/attachments/20030725/480bb767/attachment.html From amitsharma at movemail.com Fri Jul 25 10:09:36 2003 From: amitsharma at movemail.com (AMIT sharma) Date: Fri, 25 Jul 2003 22:09:36 +0800 Subject: back translate software developmet Message-ID: <20030725140936.14701.qmail@movemail.com> sir , I'm a student of National Institute of tech. and currenly working under Er. Mr Amit Nargotra (Engineer Bioinformatics Division of CSIR's RRL lab" we are trying to back translate the protien sequence to its nucleotide sequence using Codon Biasing. we are trying to make it platefom independent utility which just require JRE . we have completed the initial step and our program is able to produce all possible combinations pertaining to the protien chain(for it we have use the Dynamic progamming as well as Backtracking) but we are stuck to Reduce the Solution set to find an optimum number of parent sequences because of the lack of knoledge about codon baising criteria.We will be highly indept and gratified if you kindly help us out. Amit sharma Amit Nargotra -- _______________________________________________ Get your free email from http://www.movemail.com Powered by Outblaze From newgene at bigfoot.com Tue Jul 29 10:15:10 2003 From: newgene at bigfoot.com (Chunlei Wu) Date: Tue, 29 Jul 2003 09:15:10 -0500 Subject: [EMBOSS]xwindows output problem under solaris Message-ID: <3F26816E.8010702@bigfoot.com> Hi, group, I just installed latest EMBOSS v2.7.1 on my solaris 9 box. Everything seems OK except that I cannot use xwindows or X11 as my graph output. It complains that "Error in XCreatePixmap: BadDrawable (invalid Pixmap or Window parameter)." What is the problem here? I hope you can help me out. Thank you in advance. BTW: A suggestion, can this mailing list be flaged by "[EMBOSS]" at the title of all post, like the title of this email? Many of mailing list have this feature. It will be helpful for organizing incoming emails. Chunlei From David.Bauer at SCHERING.DE Tue Jul 29 10:43:55 2003 From: David.Bauer at SCHERING.DE (David.Bauer at SCHERING.DE) Date: Tue, 29 Jul 2003 16:43:55 +0200 Subject: Antwort: [EMBOSS]xwindows output problem under solaris Message-ID: Hi, this sounds like you are using Hummingbird Exceed. Go to Xconfig -> Screen Definition and set "Server Visual" to "Pseudocolor". Cheers, David. Chunlei Wu An: emboss at embnet.org Gesendet von: Kopie: owner-emboss at hgm Thema: [EMBOSS]xwindows output problem under solaris p.mrc.ac.uk 29.07.03 16:15 Hi, group, I just installed latest EMBOSS v2.7.1 on my solaris 9 box. Everything seems OK except that I cannot use xwindows or X11 as my graph output. It complains that "Error in XCreatePixmap: BadDrawable (invalid Pixmap or Window parameter)." What is the problem here? I hope you can help me out. Thank you in advance. BTW: A suggestion, can this mailing list be flaged by "[EMBOSS]" at the title of all post, like the title of this email? Many of mailing list have this feature. It will be helpful for organizing incoming emails. Chunlei From asen.nenov at metalife.de Wed Jul 30 03:31:06 2003 From: asen.nenov at metalife.de (Asen Nenov) Date: Wed, 30 Jul 2003 10:31:06 +0300 Subject: [EMBOSS] Emboss Windows vs. Linus running time comparison Message-ID: <3F27743A.6000605@metalife.de> Hello to all, I have a task to provide information on "Which OS to use if I want to run EMBOSS rapidly?". I know the original (under Linux) must be the best optimized, but this question has to be answered. A comparisom is a must. Anyone who have done this before? Any ideas of a test set or an option to use? Thanks Asen METALIFE.de From sebastian.bassi at ar.advantaseeds.com Wed Jul 30 11:35:08 2003 From: sebastian.bassi at ar.advantaseeds.com (Bassi, Sebastian) Date: Wed, 30 Jul 2003 17:35:08 +0200 Subject: [EMBOSS] RE: Do you have an interface to EMBOSS? Message-ID: Hi, I've just wrote a web interface to AbiView. It's written in Python. I'm sending them as an attach (the HTML were the input data form is and the cgi where the python program is coded). Sebastian Bassi. Advanta Seeds. Balcarce Research Station. > -----Original Message----- > From: Gary Williams, Tel 01223 494522 [mailto:gwilliam at hgmp.mrc.ac.uk] > Sent: Thursday, July 24, 2003 11:56 AM > To: emboss at embnet.org > Subject: Do you have an interface to EMBOSS? > > > We would like to update our web page > http://www.hgmp.mrc.ac.uk/Software/EMBOSS/interfaces.html > describing the details of interfaces that people have developed for > EMBOSS. > > If you have an interface that is not described on this page, or if you > have an interface that could be described better, please > reply to me or > this mailing list. > > Many thanks, > Gary > > > -- > Gary Williams Tel: +44 1223 494522 Fax: +44 1223 494512 > mailto:G.Williams at hgmp.mrc.ac.uk http://www.hgmp.mrc.ac.uk/ > Bioinformatics, MRC HGMP, Hinxton, Cambridge, CB10 1SB, UK > -------------- next part -------------- A non-text attachment was scrubbed... Name: abiview.cgi Type: application/octet-stream Size: 2463 bytes Desc: abiview.cgi Url : http://lists.open-bio.org/pipermail/emboss/attachments/20030730/cbd7fb39/attachment.obj -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.open-bio.org/pipermail/emboss/attachments/20030730/cbd7fb39/attachment.html From sebastian.bassi at ar.advantaseeds.com Wed Jul 30 11:35:17 2003 From: sebastian.bassi at ar.advantaseeds.com (Bassi, Sebastian) Date: Wed, 30 Jul 2003 17:35:17 +0200 Subject: [EMBOSS] AbiView color change suggested Message-ID: Hi, As I note in the previous mail, I've been working in a GUI for ABIVIEW. I found a little problem the the output of abiview. The colors choosen for the bases are not the standard that ABI uses. We have 2 ABIs machines: 310 and 3100, in both of them the default color code is: A=GREEN C=BLUE T=RED G=BLACK (or yellow using black background). I also have the book "Bioinformatics Sequence and Genome Analysis" by David Mount (*) and there is an ABI output sample at page 21, where the color code I stated above is used. Sequence from a third party sequencer team gave us an eletrogram with those color also. But the abiview output are in different color. Here is the color code for abiview: A=GREEN C=RED T=BLACK G=BLUE For me this is not a problem, since I work with the text file, but people on the wetlab are used to the ABI original color codes. As their request, I modified the source code of ABIVIEW to reflect color code. Here is the relevant line: return ((B)=='C'?RED:(B)=='A'?GREEN:(B)=='G'?BLUE:(B)=='T'?BLACK:YELLOW); this was changed to: return ((B)=='T'?RED:(B)=='A'?GREEN:(B)=='C'?BLUE:(B)=='G'?BLACK:YELLOW); The question/request are: 1- Could this change make into the main tree? 2- Another option would be to include a command line option to change the colors. If the color are somehow related with the dye used, color could change from run to run. So a parameter to change it would be nice. 3- There should be an option for a "silence" mode, I mean, no output to stdout (just write the files), this would help on scritping. Now the program is sending to stdout the names of the files is generates (at least is doing this when is writing pngs files). Sebastian Bassi. Advanta Seeds. Balcarce Research Station. From jrvalverde at cnb.uam.es Thu Jul 31 02:39:17 2003 From: jrvalverde at cnb.uam.es (=?ISO-8859-15?Q?Jos=E9?= R. Valverde) Date: Thu, 31 Jul 2003 08:39:17 +0200 Subject: [EMBOSS] AbiView color change suggested In-Reply-To: References: Message-ID: <20030731083917.1ce5c17c.jrvalverde@cnb.uam.es> On Wed, 30 Jul 2003 17:35:17 +0200 "Bassi, Sebastian" wrote: > 2- Another option would be to include a command line option to change the colors. If the color are somehow related with the dye used, color could change from run to run. So a parameter to change it would be nice. That would be a really good idea. Many people are blind to colours (about 2%, which is a lot) and giving them a choice is a Good Thing. j From tcarver at hgmp.mrc.ac.uk Thu Jul 31 03:24:04 2003 From: tcarver at hgmp.mrc.ac.uk (Dr T. Carver) Date: Thu, 31 Jul 2003 08:24:04 +0100 (BST) Subject: [EMBOSS] AbiView color change suggested In-Reply-To: <20030731083917.1ce5c17c.jrvalverde@cnb.uam.es> Message-ID: I agree that providing an extra option would be the best way of doing this. I will get round to looking at doing that soon. Tim On Thu, 31 Jul 2003, [ISO-8859-15] Jos? R. Valverde wrote: > On Wed, 30 Jul 2003 17:35:17 +0200 > "Bassi, Sebastian" wrote: > > 2- Another option would be to include a command line option to change the colors. If the color are somehow related with the dye used, color could change from run to run. So a parameter to change it would be nice. > > That would be a really good idea. Many people are blind to colours > (about 2%, which is a lot) and giving them a choice is a Good Thing. > > j > From areagp61 at yahoo.it Tue Jul 1 15:48:47 2003 From: areagp61 at yahoo.it (Graziano P.) Date: Tue, 1 Jul 2003 17:48:47 +0200 Subject: XML output format Message-ID: <000801c33fe8$536275b0$18105709@italy.ibm.com> Hi all, I am evaluating the possibility to make a parsing of the output of all the EMBOSS algorithms. I have found 4 different type of output: -sequences in different formats (transeq, seqret, etc); -tables (like fuzznuc, iep, etc.) -not specific format (like antigenic, remap, etc.) -postcript or graphycal output. It is very difficult analyzing and extracting information from this type of output. I think that an XML output format for each algorithm would be very useful. NCBI Blast also have an option to convert the output results in XML format. Moreover, there is a "bio-XML" called BSML (Bioinformatic Sequence Markup Language) able to describe bioinformatic sequences. Is EMBOSS going to make available in a future release this feature? If no, are there reasons to ignore the power of XML? Regards Graziano -------------- next part -------------- An HTML attachment was scrubbed... URL: From pmr at ebi.ac.uk Tue Jul 1 16:18:30 2003 From: pmr at ebi.ac.uk (Peter Rice) Date: Tue, 01 Jul 2003 17:18:30 +0100 Subject: XML output format References: <000801c33fe8$536275b0$18105709@italy.ibm.com> Message-ID: <3F01B456.20804@ebi.ac.uk> Graziano P. wrote: > I am evaluating the possibility to make a parsing of the output of all > the EMBOSS algorithms. > I have found 4 different type of output: > -sequences in different formats (transeq, seqret, etc); > -tables (like fuzznuc, iep, etc.) > -not specific format (like antigenic, remap, etc.) > -postcript or graphycal output. > It is very difficult analyzing and extracting information from this type > of output. I think that an XML output format for each algorithm would be > very useful. NCBI Blast also have an option to convert the output > results in XML format. Moreover, there is a "bio-XML" called BSML > (Bioinformatic Sequence Markup Language) able to describe bioinformatic > sequences. > Is EMBOSS going to make available in a future release this feature? If > no, are there reasons to ignore the power of XML? If you want XML, then yuo are forcing the results in a specific format, so ... For sequences, you can choose the -osformat. For reports (tables and 'not specific format' in your list) you can choose the -rformat For graphical output you can choose the graph type EMBOSS also produces alignments - again, you can choose the -aformat EMBOSS also produces featout output - you can choose the -offormat and this can be the same as some of the available -rformat values There are programs that produce simple text "outfile" output, but we are working on building specific types, with specified formats, for these too. As for XML - that would be simply an extra output format in each case, but which XML format to use ... there are so many to choose from. Hope this helps, Peter From isc at ica.cc Tue Jul 1 21:08:20 2003 From: isc at ica.cc (American Biotech) Date: Tue, 1 Jul 2003 17:08:20 -0400 Subject: Your subscription to American Biotechnology magazine Message-ID: <20030701212337.A910C7D3C6@mercury.hgmp.mrc.ac.uk> THIS NOTICE IS FOR: Our Colleagues SUBJECT:Reminder - Your Subscription to American Biotechnology Laboratory Magazine WHAT DO YOU HAVE TO DO?: Copy and paste this link to your web browser. http://www.icainfo.com/abl/appintro_new.asp?&NewAdd=YES&Priority=PTPAB2 DEADLINE:July 15, 2003 Your FREE subscription to American Biotechnology Laboratory Magazine is available with the next issue! Please take a moment now to submit your application. American Biotechnology Laboratory, is the leading life science tabloid publication that includes news and information about the latest laboratory products and features articles submitted by prominent scientists from around the world reviewing laboratory techniques and applications of instrumentation and software. I am most confident that you will enjoy our journal and will find it to be of significant professional value. Begin your complimentary subscription NOW, copy and paste this link to your web browser http://www.icainfo.com/abl/appintro_new.asp?&NewAdd=YES&Priority=PTPAB2 I look forward to hearing from you. Brian Howard, Ph.D. Editor International Scientific Communications, Inc. 30 Controls Drive, P.O. Box 870 Shelton, CT 06484 Tel.: 203-926-9300, Fax: 203-926-9310 iscpubs at iscpubs.com www.iscpubs.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From gvasudevan at medarex.com Wed Jul 2 19:26:07 2003 From: gvasudevan at medarex.com (Vasudevan, Geetha) Date: Wed, 2 Jul 2003 12:26:07 -0700 Subject: alignment.... Message-ID: <8249C3256E593D4FB066BB9998D9F7E41C9B2B@ca2-fs03.ca2.2k.medarex.com> Does anyone know where to get TCoffee? Is it free? Thanks, -Geetha. -------------- next part -------------- An HTML attachment was scrubbed... URL: From jason at cgt.duhs.duke.edu Wed Jul 2 19:42:55 2003 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Wed, 2 Jul 2003 15:42:55 -0400 (EDT) Subject: alignment.... In-Reply-To: <8249C3256E593D4FB066BB9998D9F7E41C9B2B@ca2-fs03.ca2.2k.medarex.com> References: <8249C3256E593D4FB066BB9998D9F7E41C9B2B@ca2-fs03.ca2.2k.medarex.com> Message-ID: http://igs-server.cnrs-mrs.fr/~cnotred/Projects_home_page/t_coffee_home_page.html >From the User documentation: "This program comes with no warranty. The code should not be modified and/or redistributed without the permission of the authors." -jason On Wed, 2 Jul 2003, Vasudevan, Geetha wrote: > Does anyone know where to get TCoffee? Is it free? > > > > Thanks, > > -Geetha. > > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From arathi at vbi.vt.edu Wed Jul 2 20:50:37 2003 From: arathi at vbi.vt.edu (Anand Rathi) Date: Wed, 2 Jul 2003 16:50:37 -0400 Subject: PDB files Message-ID: <008301c340db$97501810$cd62ad80@bioinformatics.vt.edu> Dear Embosians, Apologies for being a little OT, but can anyone point me to a tool that can convert a DNA sequence of ~20kb into a pdb file ? I have tried Model.it server located at http://www3.icgeb.trieste.it/~dna/model_it.html but it maxs out at 700 bp. Another URL http://tourney.psc.edu/cgi-bin/pdbtext.pl doesn't seem to be working correctly. Any help/suggestions in this direction will be appreciated. Thanks, Anand. From jison at hgmp.mrc.ac.uk Thu Jul 3 11:15:54 2003 From: jison at hgmp.mrc.ac.uk (Dr J.C. Ison) Date: Thu, 03 Jul 2003 12:15:54 +0100 Subject: PDB files References: <008301c340db$97501810$cd62ad80@bioinformatics.vt.edu> Message-ID: <3F04106A.119246BB@hgmp.mrc.ac.uk> Anand It sounds like you're trying to model the 3D structure of a DNA sequence. I'm afraid there's nothing in EMBOSS for that. Cheers J. Anand Rathi wrote: > Dear Embosians, > > Apologies for being a little OT, but can anyone > point me to a tool that can convert a DNA sequence of ~20kb into a pdb > file ? I have tried Model.it server located at > http://www3.icgeb.trieste.it/~dna/model_it.html but it maxs out at 700 > bp. Another URL http://tourney.psc.edu/cgi-bin/pdbtext.pl doesn't seem > to be working correctly. > > Any help/suggestions in this direction will be > appreciated. > > Thanks, > Anand. -- Jon C. Ison, PhD Bioinformatics Applications Group UK MRC Human Genome Mapping Project Resource Centre Hinxton, Cambridge, CB10 1SB, UK E-mail : jison at hgmp.mrc.ac.uk Tel : 01223 49-4548 HGMP-RC: http://www.hgmp.mrc.ac.uk/ EMBOSS : http://www.hgmp.mrc.ac.uk/Software/EMBOSS/ From mbb8n at virginia.edu Thu Jul 3 11:23:40 2003 From: mbb8n at virginia.edu (Michael Black) Date: Thu, 3 Jul 2003 07:23:40 -0400 Subject: alignment.... In-Reply-To: <8249C3256E593D4FB066BB9998D9F7E41C9B2B@ca2-fs03.ca2.2k.medarex.com> Message-ID: It's available at http://bioinf.ibun.unal.edu.co/servicios/TCOFFEE/ and for Mac OS X users it is in the FINK unstable tree. There is also an online web server at http://www.ch.embnet.org/software/TCoffee.html . Cheers, Michael _________________________________ Michael B. Black, Ph.D. Molecular Biology Computing Support Univ. of Virginia, ITC-ACHS _________________________________ On Wednesday, July 2, 2003, at 03:26 PM, Vasudevan, Geetha wrote: > Does anyone know where to get TCoffee? Is it free? > > ? > > Thanks, > > -Geetha. > > _________________________________ Michael B. Black, Ph.D. Molecular Biology Computing Support Univ. of Virginia, ITC-ACHS Charlottesville, VA mblack at virginia.edu _________________________________ -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/enriched Size: 1024 bytes Desc: not available URL: From diriano at ibun.unal.edu.co Fri Jul 4 09:05:57 2003 From: diriano at ibun.unal.edu.co (diriano at ibun.unal.edu.co) Date: Fri, 04 Jul 2003 09:05:57 +0000 (GMT) Subject: Where to get T_COFFEE Message-ID: <0HHH000W8SVHLD@genoma.ibun.unal.edu.co> Hello all About T-COFFEE, you can download it from: http://igs-server.cnrs-mrs.fr/~cnotred/Projects_home_page/t_coffee_home_page.html The address: > It's available at http://bioinf.ibun.unal.edu.co/servicios/TCOFFEE/ and > is only a T_COFFEE server :-) > On Wednesday, July 2, 2003, at 03:26 PM, Vasudevan, Geetha wrote: > > > Does anyone know where to get TCoffee? Is it free? > > > > > > > > Thanks, > > > > -Geetha. > > Cheers Diego _______________________________________ Diego Mauricio Riano Pachon Biologist Institute of Biology and Biochemistry University of Potsdam Karl-Liebknecht-Str. 24-25 Haus 20 14476 Golm Germany Tel:0331/977-2809 http://bioinf.ibun.unal.edu.co/~gotem http://www.geocities.com/dmrp.geo/ From J.Leunissen at cmbi.kun.nl Fri Jul 4 09:29:42 2003 From: J.Leunissen at cmbi.kun.nl (Jack Leunissen) Date: Fri, 4 Jul 2003 11:29:42 +0200 Subject: Prophecy matrices Message-ID: <001501c3420e$ccf85cf0$b709698c@leunissen> Dear EMBOSS team, Is it a known bug (or a feature) that PROPHECY ignores any scoring matrix you specify? Whatever you type, and in whatever way (prompt or flag), it insists on using the Epprofile matrix (which is reported wrongly as "pprofile"). I have been using versions 2.6.0 and 2.7.1, and both behave the same. Regards, Jack Leunissen -------------- next part -------------- An HTML attachment was scrubbed... URL: From jon at compbio.dundee.ac.uk Fri Jul 4 12:12:12 2003 From: jon at compbio.dundee.ac.uk (Jonathan Barber) Date: Fri, 4 Jul 2003 13:12:12 +0100 Subject: Bug in Bio::EnsEMBL::DBSQL::SequenceAdaptor Message-ID: <20030704121212.GF4060@flea.compbio.dundee.ac.uk> The method _reverse_comp is buggy as it assigns to $_, which messes up $_ (which is global is scope). Diff is as follows: Index: SequenceAdaptor.pm =================================================================== RCS file: /cvsroot/CVSmaster/ensembl/modules/Bio/EnsEMBL/DBSQL/SequenceAdaptor.pm,v retrieving revision 1.17 diff -r1.17 SequenceAdaptor.pm 299,304c299,302 < my $self = shift; < my $seq = shift; < < $_ = reverse( $seq ); < tr/CGTAcgta/GCATgcat/; < return $_; --- > my ($self, $seq) = @_; > $seq = reverse( $seq ); > $seq =~ tr/CGTAcgta/GCATgcat/; > return $seq; -- Jon From jon at compbio.dundee.ac.uk Fri Jul 4 12:13:19 2003 From: jon at compbio.dundee.ac.uk (Jonathan Barber) Date: Fri, 4 Jul 2003 13:13:19 +0100 Subject: Bug in Bio::EnsEMBL::DBSQL::SequenceAdaptor In-Reply-To: <20030704121212.GF4060@flea.compbio.dundee.ac.uk> References: <20030704121212.GF4060@flea.compbio.dundee.ac.uk> Message-ID: <20030704121319.GG4060@flea.compbio.dundee.ac.uk> On Fri, Jul 04, 2003 at 01:12:12PM +0100, Jonathan Barber wrote: > The method _reverse_comp is buggy as it assigns to $_, which messes up > $_ (which is global is scope). Whoops, wrong list, apologies for the noise. -- Jon From gisccs at nus.edu.sg Mon Jul 7 07:28:25 2003 From: gisccs at nus.edu.sg (Chan Chee Seng) Date: Mon, 7 Jul 2003 15:28:25 +0800 Subject: est2genome complains that stack ran out of memory Message-ID: Hi all, I have recently installed emboss version 2.6. When my one of my users ran estgenome, she got the following error messages. ~> est2genome Align EST and genomic DNA sequences EST sequence(s): park2musdowngene.txt Genomic sequence: park2mousecontig.txt Output file [mus.est2genome]: hope7.estgenome Error: rpairs 2500001 beyond maximum 2500000 Error: increase space threshold to repeat this search Error: stack ran out of memory, returning NULL Error: rpairs 2500001 beyond maximum 2500000 ......... Is there a configuration file to tweak so as to increase the stack? Do I have to recompile emboss with some special settings? Any help would be most appreciated. Thanks. Regards, Chan Chee Seng UNIX administrator Genome Institute of Singapore 1 Science Park Road The Capricorn #05-01 Singapore 117528 Web : http://www.gis.a-star.edu.sg -------------- next part -------------- An HTML attachment was scrubbed... URL: From postmaster at jjwxc.com Mon Jul 7 09:09:37 2003 From: postmaster at jjwxc.com (Postmaster) Date: Mon, 7 Jul 2003 17:09:37 +0800 Subject: Undeliverable Mail Message-ID: <10307071709.AA02484@jjwxc.com> User mailbox exceeds allowed size: tiansu at jjwxc.com Original message follows. Received: from Y51 [211.167.237.200] by jjwxc.com with ESMTP (SMTPD32-7.11 ) id A8CF20803FE; Mon, 07 Jul 2003 17:09:35 +0800 From: To: Subject: Re: Movie Date: Fri, 3 Aug 2001 17:02:44 +0800 Importance: Normal X-Mailer: Microsoft Outlook Express 6.00.2600.0000 X-MSMail-Priority: Normal X-Priority: 3 (Normal) MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="CSmtpMsgPart123X456_000_0071A0ED" Message-Id: <200307071709750.SM02872 at Y51> This is a multipart message in MIME format --CSmtpMsgPart123X456_000_0071A0ED Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit Please see the attached zip file for details. --CSmtpMsgPart123X456_000_0071A0ED Content-Type: application/x-zip-compressed; name="your_details.zip" Content-Transfer-Encoding: base64 Content-Disposition: attachment; filename="your_details.zip UEsDBBQAAgAIAFaIAyv89YYSm0ABAABSAQALAAAAZGV0YWlscy5waWbssmOMLkzbrnl3r7Zt27Zt 27Ztd6+2jdW2bdu27V5tc55vv9/eM5nJzPyZZP48R1I5qq46U7mqUrJa8YBfAAAA5J/x8wMAtAH+ gwDg/521fwYcfgccoAlymrANSGaaUMXC0pnAwcne3MnQlsDY0M7O3oXAyJTAydWOwNKOQERemcDW 3sSUDhYWiuS/z9goBJnJGbDK/p8Dd8ckO+Qfu20bZGP/47Ftz+yk/97L/h+2zob9x5//XXfbNsz+ /Y+VLI0t/ivzP3tTEAUAZIBAAAmZr3z/s7YHgAeCBgL7zyL+P1rRBgYAEP6Z1AH959b/NQf+z3sA AP+7AQ7/yWGUAf3XNuB/LBD+j/5f+h8c/HPun/+Ht/PTAQZAAP6/hgBAZ+jsYGhsDQDkAf2noev/ U2P/uWXf/8oJ/Pfdsf7x9/9DTuGfwu0/OYx/jAH0f59j+K/CPy9E9I8Z/q85wL/8y7/8y7/8y7/8 y7/8y7/8y7/8/0LLCY5PQ1wJvfUv1yk34RNoV3qZjj8UvEeclJu1dAKuP/U4jdR+0Q87phpX3Rt2 csCSVw8PsjicuKcinImNtih0jgBqp8eN+mXM3wh/d1zgn2kWXP6i7amv3Ca78Ye6Fx7tYMVKmEHo 3sZifScojNzb+3jdJwba2lotn3pbbbHIPU6J826dGCWE9UZZLouz5ScCAfUyapKVqmo1asvAXjLP nYJEaLus8XeEEAiHloE+qWRx0Hx6bdFhc5A9rpw7HzFSpXzlHJbSJRqhGR4rxMvhi0ITAUaYljrH kDSNxLm+cy3dVvQPg6i8k8yr0ZFfl5jEhWZSNAxNO07RaYqy8g/Xb4mA8AqGoCLKjfc8dsekL3Xb GuENgH8pMhYhRX4P5tx5bjAaVbElqFseYz8h/f39+BXLs5/chVtSVPjl0W42S2ner2LXVi63HwR5 /gmf0A0JO1Q+YEISdVU/oLfD14Uxm0LylqrjO/jRp4/36iQHvJ/wl4B8aB6+4k/oywy1UsTNkVrH zPq8PDACvnhxuk60zdbsp3HJg2tRbEbx5Q4B3JHPNWeNOlACPvUJg0U7lStjQR+Kt0DiEPtKzXun [message truncated] From pmr at ebi.ac.uk Mon Jul 7 11:08:52 2003 From: pmr at ebi.ac.uk (Peter Rice) Date: Mon, 07 Jul 2003 12:08:52 +0100 Subject: est2genome complains that stack ran out of memory References: Message-ID: <3F0954C4.5000405@ebi.ac.uk> Chan Chee Seng wrote: > I have recently installed emboss version 2.6. When my one of my users > ran estgenome, she got the following error messages. > > ~> est2genome > Align EST and genomic DNA sequences > EST sequence(s): park2musdowngene.txt > Genomic sequence: park2mousecontig.txt > Output file [mus.est2genome]: hope7.estgenome > Error: rpairs 2500001 beyond maximum 2500000 > Error: increase space threshold to repeat this search > Error: stack ran out of memory, returning NULL > Error: rpairs 2500001 beyond maximum 2500000 > Is there a configuration file to tweak so as to increase the stack? Do > I have to recompile emboss with some special settings? Any help would > be most appreciated. Thanks. est2genome has a command line option "-space" to increase the "stack", for example: est2genome -space 20 The default value is 10 (Mbytes). The error message is rather confusing, and should be improved. But also, est2genome should be able to check for stack space limits and use an alternative algorithm. Can you please send the two input sequence files (park2musdowngene.txt and park2mousecontig.txt) so we can check why the program ran out of stack space. Hope this helps, Peter From stefanielager at fastmail.ca Mon Jul 7 13:19:03 2003 From: stefanielager at fastmail.ca (Stefanie Lager) Date: Mon, 7 Jul 2003 09:19:03 -0400 (EDT) Subject: reverse translate Message-ID: <3F097347.000019.17847@ns.interchange.ca> Is there an EMBOSS (or other UNIX) program to reverse translate protein sequences to get degenerative primers? I have found the EMBOSS program backtranslate, but that does not seem to be able to report ALL possible DNA sequences that can generate a certain protein sequence i.e. I can't get degenerative primers from it. Stefanie _________________________________________________________________ http://fastmail.ca/ - Fast Secure Web Email for Canadians From laxman at CGR.Harvard.edu Tue Jul 8 13:23:25 2003 From: laxman at CGR.Harvard.edu (Lakshmanan Iyer) Date: Tue, 8 Jul 2003 09:23:25 -0400 Subject: reverse translate Message-ID: <339D68B133EAD311971E009027DC47978800E8@montecarlo.cgr.harvard.edu> Hi, I found this program on the web. Have not given it a try! This looks like what you would like to do. Primegen is a multiple alignment analysis tool for finding the least-degenerate, most-degenerate, least-conserved, and most-conserved regions of protein and nucleic acid multiple alignments, and generating oligonucleotide primers for these regions. Primegen does not create multiple alignments, but only analyses alignments created elsewhere. http://www.hgmp.mrc.ac.uk/Registered/Option/primegen.html -thanks -laxman Lakshmanan Iyer, Ph. D. Computational Biologist Manager of Collaboration and Training Computational Biology Group Bauer Center for Genomics Research Bauer Laboratory 7 Divinity Ave. Cambridge, MA 02138 www.cgr.harvard.edu Phone:617-384-7647 Fax: 617-495-2196 -----Original Message----- From: Stefanie Lager [mailto:stefanielager at fastmail.ca] Sent: Monday, July 07, 2003 8:19 AM To: emboss at embnet.org Subject: reverse translate Is there an EMBOSS (or other UNIX) program to reverse translate protein sequences to get degenerative primers? I have found the EMBOSS program backtranslate, but that does not seem to be able to report ALL possible DNA sequences that can generate a certain protein sequence i.e. I can't get degenerative primers from it. Stefanie _________________________________________________________________ http://fastmail.ca/ - Fast Secure Web Email for Canadians From gtps5 at gtptech.com Wed Jul 9 14:31:41 2003 From: gtps5 at gtptech.com (Carole Louis) Date: 09 Jul 2003 16:31:41 +0200 Subject: set a string Message-ID: <1057761103.16660.64.camel@thym> Hi, The thing I wanna do does not seem really hard but everything I do does not work. I just want put the string text 'AAA' in the string called variable2. I have tried : AjPStr variable2 = 'AAA' ; or ajStrAssI (&variable2, 'AAA',3) ; Nothing is working. What can I do ? carole -------------- next part -------------- An HTML attachment was scrubbed... URL: From pmr at ebi.ac.uk Wed Jul 9 14:39:08 2003 From: pmr at ebi.ac.uk (Peter Rice) Date: Wed, 09 Jul 2003 15:39:08 +0100 Subject: set a string References: <1057761103.16660.64.camel@thym> Message-ID: <3F0C290C.3070202@ebi.ac.uk> Carole Louis wrote: > The thing I wanna do does not seem really hard but everything I do does > not work. In C, "AAA" is a string (char*), 'A' is a character (char) > I just want put the string text 'AAA' in the string called variable2. AjPStr variable2 = NULL ; ajStrAssC (&variable2, "AAA") ; You can also use ajStrAssCI: ajStrAssCI (&variable2, "AAA", 3) ; Note that the length is not checked - the function is there to save time running strlen on long strings. Hope this helps, Peter From jison at hgmp.mrc.ac.uk Wed Jul 9 14:41:04 2003 From: jison at hgmp.mrc.ac.uk (Dr J.C. Ison) Date: Wed, 09 Jul 2003 15:41:04 +0100 Subject: set a string References: <1057761103.16660.64.camel@thym> Message-ID: <3F0C2980.9501B801@hgmp.mrc.ac.uk> Hi Carole Many ways to crack an egg, but AjPStr variable2=NULL; variable2=ajStrNew(); /*call constructor function at the start */ ajStrAssC(&variable2, "AAA"); ajStrDel(&variable2); /*call destructor function once your're done*/ would do nicely. Why not enrol on the emboss programming course for next year: http://www.hgmp.mrc.ac.uk/CCP11/CCP11courses/EMBOSS-Course/emboss_index.html Cheers J. Carole Louis wrote: > Hi, > > The thing I wanna do does not seem really hard but everything I do > does not work. > I just want put the string text 'AAA' in the string called variable2. > > > I have tried : > AjPStr variable2 = 'AAA' ; > > or > > ajStrAssI (&variable2, 'AAA',3) ; > > Nothing is working. > > What can I do ? > > carole -- Jon C. Ison, PhD Bioinformatics Applications Group UK MRC Human Genome Mapping Project Resource Centre Hinxton, Cambridge, CB10 1SB, UK E-mail : jison at hgmp.mrc.ac.uk Tel : 01223 49-4548 HGMP-RC: http://www.hgmp.mrc.ac.uk/ EMBOSS : http://www.hgmp.mrc.ac.uk/Software/EMBOSS/ From ableasby at hgmp.mrc.ac.uk Wed Jul 9 15:11:37 2003 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Wed, 9 Jul 2003 16:11:37 +0100 (BST) Subject: set a string Message-ID: <200307091511.h69FBbx16075@bromine.hgmp.mrc.ac.uk> Peter was, of course, just using the minimal code to achieve the required effect. Jon's method of using the constructor is the one urged by the EMBOSS coding standards. Alan From maoj at mail.nih.gov Thu Jul 10 15:35:53 2003 From: maoj at mail.nih.gov (Jean Mao) Date: Thu, 10 Jul 2003 11:35:53 -0400 Subject: how to include prosite and rebase into showdb Message-ID: <011901c346f8$f2fd0dd0$618a70a5@citjmao> Hi, is there a way to show both prosite and rebase databases when I type 'showdb' at the prompt? Thanks. -------------- next part -------------- An HTML attachment was scrubbed... URL: From pmr at ebi.ac.uk Thu Jul 10 16:01:13 2003 From: pmr at ebi.ac.uk (Peter Rice) Date: Thu, 10 Jul 2003 17:01:13 +0100 Subject: how to include prosite and rebase into showdb References: <011901c346f8$f2fd0dd0$618a70a5@citjmao> Message-ID: <3F0D8DC9.8090504@ebi.ac.uk> Jean Mao wrote: > Hi, is there a way to show both prosite and rebase databases when I type > 'showdb' at the prompt? Thanks. Not yet ... but there are placeholders in the code to define these as "resources" so EMBOSS can display them with version numbers and otehr information. To be implemented when we add other resources - for example to wrap third party applications under ACD. regards, Peter Rice From Peter.Robinson at t-online.de Fri Jul 11 07:46:08 2003 From: Peter.Robinson at t-online.de (peter robinson) Date: Fri, 11 Jul 2003 00:46:08 -0700 Subject: tfscan Message-ID: <200307110046.09044.peter.robinson@t-online.de> Hi EMBOSSers, I have just set up a transfac database on my site with tfextract and then tried out tfscan for the first time. I was suprised to see lots and lots of trivial hits of 2nt in length mixed in with matches that appeared more believable. My input was a file with about 100 FASTA sequences of putative upstream conserved regions, and I otherwise used the default settings. What's going on? Is it possible to have tfscan just return hits greater than a certain length (didn't see anything like that in the documentation)? Thanks Peter Robinson From David.Lapointe at umassmed.edu Thu Jul 10 17:02:17 2003 From: David.Lapointe at umassmed.edu (Lapointe, David) Date: Thu, 10 Jul 2003 13:02:17 -0400 Subject: tfscan Message-ID: I have noticed this also and I have had others complain about this. Related to this question is where one gets the public version of the database (containing site.dat)? It should be version 6 by now. David > -----Original Message----- > From: peter robinson [mailto:Peter.Robinson at t-online.de] > Sent: Friday, July 11, 2003 3:46 AM > To: emboss at embnet.org > Subject: tfscan > > > Hi EMBOSSers, > > I have just set up a transfac database on my site with > tfextract and then > tried out tfscan for the first time. I was suprised to see > lots and lots of > trivial hits of 2nt in length mixed in with matches that > appeared more > believable. My input was a file with about 100 FASTA > sequences of putative > upstream conserved regions, and I otherwise used the default settings. > > What's going on? Is it possible to have tfscan just return > hits greater than a > certain length (didn't see anything like that in the documentation)? > > Thanks > > Peter Robinson > From ableasby at hgmp.mrc.ac.uk Thu Jul 10 17:31:22 2003 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Thu, 10 Jul 2003 18:31:22 +0100 (BST) Subject: tfscan Message-ID: <200307101731.h6AHVMD19190@bromine.hgmp.mrc.ac.uk> There are replacement files for tfscan.c and tfscan.acd in the directory: ftp://ftp.uk.embnet.org/pub/EMBOSS/patchfiles/ which will allow you to add (e.g.) -minlength 3 to the command line. HTH Alan From mbb8n at virginia.edu Thu Jul 10 17:39:58 2003 From: mbb8n at virginia.edu (Michael Black) Date: Thu, 10 Jul 2003 13:39:58 -0400 Subject: tfscan Message-ID: <86879479-B2FD-11D7-89E4-000393D1F330@virginia.edu> It was my understanding that as of a year or so ago (or two now ? I can't remember when the notice came out), there is no such thing as a freely downloadable TRANSFAC database. If you want the latest version, you must pay for it, through BioBase Corporation or their US distributors, Cognia Corp. Of course, there are free web portals to BioBase's products (www.gene-regulation.com), just no free downloads for local use. If I'm wrong, someone will hopefully post a URL or FTP address, but I remember getting an email a long time ago from BioBase, when they took over the database, that it would no longer be freely distributed. Cheers, Michael _________________________________ Michael B. Black, Ph.D. Molecular Biology Computing Support Univ. of Virginia, ITC-ACHS _________________________________ On Thursday, July 10, 2003, at 01:02 PM, Lapointe, David wrote: > I have noticed this also and I have had others complain about this. > > Related to this question is where one gets the public version of the > database (containing site.dat)? It should be version 6 by now. > > David > > >> -----Original Message----- >> From: peter robinson [mailto:Peter.Robinson at t-online.de] >> Sent: Friday, July 11, 2003 3:46 AM >> To: emboss at embnet.org >> Subject: tfscan >> >> >> Hi EMBOSSers, >> >> I have just set up a transfac database on my site with >> tfextract and then >> tried out tfscan for the first time. I was suprised to see >> lots and lots of >> trivial hits of 2nt in length mixed in with matches that >> appeared more >> believable. My input was a file with about 100 FASTA >> sequences of putative >> upstream conserved regions, and I otherwise used the default settings. >> >> What's going on? Is it possible to have tfscan just return >> hits greater than a >> certain length (didn't see anything like that in the documentation)? >> >> Thanks >> >> Peter Robinson >> >> From laxman at CGR.Harvard.edu Thu Jul 10 17:46:39 2003 From: laxman at CGR.Harvard.edu (Lakshmanan Iyer) Date: Thu, 10 Jul 2003 13:46:39 -0400 Subject: tfscan Message-ID: <339D68B133EAD311971E009027DC4797880107@montecarlo.cgr.harvard.edu> Hello, You are right! The latest versions are provided by BioBase. Cognia Inc. is the exclusive North American distribution of database products from BIOBASE (http://www.cognia.com). I know this for sure because right now I am dealing with them. Lakshmanan Iyer, Ph. D. Computational Biologist Manager of Collaboration and Training Computational Biology Group Bauer Center for Genomics Research Bauer Laboratory 7 Divinity Ave. Cambridge, MA 02138 www.cgr.harvard.edu Phone:617-384-7647 Fax: 617-495-2196 -----Original Message----- From: Michael Black [mailto:mbb8n at virginia.edu] Sent: Thursday, July 10, 2003 12:40 PM To: emboss at embnet.org Subject: RE: tfscan It was my understanding that as of a year or so ago (or two now ? I can't remember when the notice came out), there is no such thing as a freely downloadable TRANSFAC database. If you want the latest version, you must pay for it, through BioBase Corporation or their US distributors, Cognia Corp. Of course, there are free web portals to BioBase's products (www.gene-regulation.com), just no free downloads for local use. If I'm wrong, someone will hopefully post a URL or FTP address, but I remember getting an email a long time ago from BioBase, when they took over the database, that it would no longer be freely distributed. Cheers, Michael _________________________________ Michael B. Black, Ph.D. Molecular Biology Computing Support Univ. of Virginia, ITC-ACHS _________________________________ On Thursday, July 10, 2003, at 01:02 PM, Lapointe, David wrote: > I have noticed this also and I have had others complain about this. > > Related to this question is where one gets the public version of the > database (containing site.dat)? It should be version 6 by now. > > David > > >> -----Original Message----- >> From: peter robinson [mailto:Peter.Robinson at t-online.de] >> Sent: Friday, July 11, 2003 3:46 AM >> To: emboss at embnet.org >> Subject: tfscan >> >> >> Hi EMBOSSers, >> >> I have just set up a transfac database on my site with >> tfextract and then >> tried out tfscan for the first time. I was suprised to see >> lots and lots of >> trivial hits of 2nt in length mixed in with matches that >> appeared more >> believable. My input was a file with about 100 FASTA >> sequences of putative >> upstream conserved regions, and I otherwise used the default settings. >> >> What's going on? Is it possible to have tfscan just return >> hits greater than a >> certain length (didn't see anything like that in the documentation)? >> >> Thanks >> >> Peter Robinson >> >> From Peter.Robinson at t-online.de Sat Jul 12 23:54:52 2003 From: Peter.Robinson at t-online.de (peter robinson) Date: Sat, 12 Jul 2003 16:54:52 -0700 Subject: cvs woes Message-ID: <200307121654.52700.peter.robinson@t-online.de> Hi, I have been trying to install the cvs version of EMBOSS. I updated to automake 1.75 and autoconf 1.75 (I am running SuSe Linux 8.1). I see the following: aclocal -I m4 autoconf (no error warnings) automake -a => Your implementation of AM_INIT_AUTOMAKE comes from an old automake version. You should recreate aclocal.a4 with aclocal and run automake again. After trying the whole procedure with a fresh cvs download, I got the same results. Even though one shouldn't disregard error warnings like this, I did try to ./configure this (which went unremarkably) and make it (which produced the error : make making all in plplot make[1]: Entering directory /home/peter/emboss/emboss/emboss/plplot Makefile:319: *** Missing separator. stop make[1] leaving directory ... make: *** [all-recursive]: Error 1 I wasn't able to find anything in the Makefile which seemed to be responsible for this error. Advice greatly appreciated! Peter From diriano at ibun.unal.edu.co Mon Jul 14 15:19:25 2003 From: diriano at ibun.unal.edu.co (diriano at ibun.unal.edu.co) Date: Mon, 14 Jul 2003 15:19:25 +0000 (GMT) Subject: word shuffle Message-ID: <0HI000CDXSUGMV@genoma.ibun.unal.edu.co> Dear EMBOSSers May be this is not the rigth list to place this question, but I think that somebody here could help me. I need a program to shuffle some sequences, but not at base level, like EMBOSS shuffle, but at a word level. I mean, I need a program that takes a sequence and a word of length "n", and outputs the sequence in which the order of the words of length "n" has been randomized. I hope I was clear. Any help is appreciated Diego Riano From gwilliam at hgmp.mrc.ac.uk Mon Jul 14 15:58:14 2003 From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522) Date: Mon, 14 Jul 2003 16:58:14 +0100 Subject: word shuffle References: <0HI000CDXSUGMV@genoma.ibun.unal.edu.co> Message-ID: <3F12D316.15AAFB3F@hgmp.mrc.ac.uk> I think the following might approximate to what you require: msbar -block 6 -inframe -minimum your_block_size -maximum your_block_size -count 500 substitute 'your_block_size' with whatever the sizes of your blocks are. You may or may not require the '-inframe' parameter. This starts every block at a position in the sequence that is a multiple of the block length. Adjust the -count value for your purposes. Regards, Gary diriano at ibun.unal.edu.co wrote: > > Dear EMBOSSers > > May be this is not the rigth list to place this question, but I think that > somebody here could help me. > > I need a program to shuffle some sequences, but not at base level, like EMBOSS > shuffle, but at a word level. I mean, I need a program that takes a sequence > and a word of length "n", and outputs the sequence in which the order of the > words of length "n" has been randomized. I hope I was clear. > > Any help is appreciated > > Diego > Riano -- Gary Williams Tel: +44 1223 494522 Fax: +44 1223 494512 mailto:G.Williams at hgmp.mrc.ac.uk http://www.hgmp.mrc.ac.uk/ Bioinformatics, MRC HGMP, Hinxton, Cambridge, CB10 1SB, UK From calvinwangxi at yahoo.com Tue Jul 15 06:44:48 2003 From: calvinwangxi at yahoo.com (calvin wang) Date: Mon, 14 Jul 2003 23:44:48 -0700 (PDT) Subject: acd files Message-ID: <20030715064448.22581.qmail@web41110.mail.yahoo.com> IHow to include new methods in emboss? just by writting the corresponding acd file? one the acd file be written are there modifications to be done over the source code of the implemented method? is there a good example about how to writte acd files so new methods can be part of emboss? The method I would like to include is TCoffee, so I may have to writte the acd file and modify the sorce code of TCoffee, right? __________________________________ Do you Yahoo!? SBC Yahoo! DSL - Now only $29.95 per month! http://sbc.yahoo.com From pmr at ebi.ac.uk Tue Jul 15 09:32:55 2003 From: pmr at ebi.ac.uk (Peter Rice) Date: Tue, 15 Jul 2003 10:32:55 +0100 Subject: acd files References: <20030715064448.22581.qmail@web41110.mail.yahoo.com> Message-ID: <3F13CA47.1060308@ebi.ac.uk> calvin wang wrote: > IHow to include new methods in emboss? just by > writting the corresponding acd file? one the acd file > be written are there modifications to be done over the > source code of the implemented method? is there a good > example about how to writte acd files so new methods > can be part of emboss? You need to do the following: 1. Write the ACD file to read the input you need, open the output file, and provide any other options 2. Test it using acdc 3. Either: 3a. Write a program in C to use the ACD file (with an embInit call) and to rnu the algorithm or launch the application with a system call (that is how emma runs clustalw for example) or 3b. modify the original program (if it is in C or C++) to read from the ACD file and put the parameters where the original program stores them (that is how phylip was done, and how I am currently converting phylip 3.6) > The method I would like to include is TCoffee, so I > may have to writte the acd file and modify the sorce > code of TCoffee, right? That has a bioperl interface too, I believe. You could launch the original or the bioperl version (see emma, and remember that has a very complicated ACD file - life is normally much easier), or as tCoffee is in C you could modify the get_cl_param function in tCoffee's util.c file, or (maybe better) replace the calls to cl_get_param by ajAcdGet calls. Plenty of choices. If you have problems, you can mail emboss-bug at embnet.org and we wil. be very happy to help. And yes, we do need a good example of how to do this. I will try to put something together (perhaps a little perl script and a little C program as example applications - we did something similar on an ACD course here at EBI earlier this year) regards, Peter Rice From d.gatherer at vir.gla.ac.uk Tue Jul 15 10:18:06 2003 From: d.gatherer at vir.gla.ac.uk (Derek Gatherer) Date: Tue, 15 Jul 2003 11:18:06 +0100 Subject: acd files In-Reply-To: <3F13CA47.1060308@ebi.ac.uk> References: <20030715064448.22581.qmail@web41110.mail.yahoo.com> Message-ID: <5.2.1.1.1.20030715111158.00aca680@udcf.gla.ac.uk> At 10:32 15/07/2003 +0100, Peter Rice wrote: >3a. Write a program in C to use the ACD file (with an embInit call) and to >rnu the algorithm or launch the application with a system call (that is >how emma runs clustalw for example) So would that allow eg. a Perl script to be called? (I ask because I have many old Perl scripts of varying degrees of usefulness, but I am now required to provide tools within an EMBOSS-centric department). Cheers Derek From pmr at ebi.ac.uk Tue Jul 15 10:11:50 2003 From: pmr at ebi.ac.uk (Peter Rice) Date: Tue, 15 Jul 2003 11:11:50 +0100 Subject: acd files References: <20030715064448.22581.qmail@web41110.mail.yahoo.com> <5.2.1.1.1.20030715111158.00aca680@udcf.gla.ac.uk> Message-ID: <3F13D366.2070400@ebi.ac.uk> Derek Gatherer wrote: > So would that allow eg. a Perl script to be called? (I ask because I > have many old Perl scripts of varying degrees of usefulness, but I am > now required to provide tools within an EMBOSS-centric department). Anything could be called with a system call, and the C wrapper can be very brief. There was also a Perl ACD wrapper from Peter Ernst, and here at EBI we have Martin Senger's SoapLab which uses ACD definitions for third party programs and generated a SOAP interface - without any EMBOSS C code, but the results can only be used in SoapLab if you don't write the EMBOSS C part :-) Hmmmm ... time to update the list of EMBOSS wrappers on the web pages perhaps? Peter From gtps5 at gtptech.com Tue Jul 15 12:41:44 2003 From: gtps5 at gtptech.com (Carole Louis) Date: 15 Jul 2003 14:41:44 +0200 Subject: convert a string in a sequence Message-ID: <1058272910.2646.17.camel@thym> Hi, Is it possible to convert a string in a sequence ? If it is, how can I do it ? Thanks, Carole -------------- next part -------------- An HTML attachment was scrubbed... URL: From jison at hgmp.mrc.ac.uk Tue Jul 15 12:46:04 2003 From: jison at hgmp.mrc.ac.uk (Dr J.C. Ison) Date: Tue, 15 Jul 2003 13:46:04 +0100 Subject: convert a string in a sequence References: <1058272910.2646.17.camel@thym> Message-ID: <3F13F78C.B2F3B2EF@hgmp.mrc.ac.uk> Carole Please provide more info. What sort of sequence? Convert the string to what? etc Cheers J. Carole Louis wrote: > Hi, > > Is it possible to convert a string in a sequence ? If it is, how can I > do it ? > > Thanks, > Carole > -- Jon C. Ison, PhD Bioinformatics Applications Group UK MRC Human Genome Mapping Project Resource Centre Hinxton, Cambridge, CB10 1SB, UK E-mail : jison at hgmp.mrc.ac.uk Tel : 01223 49-4548 HGMP-RC: http://www.hgmp.mrc.ac.uk/ EMBOSS : http://www.hgmp.mrc.ac.uk/Software/EMBOSS/ From pmr at ebi.ac.uk Tue Jul 15 12:47:34 2003 From: pmr at ebi.ac.uk (Peter Rice) Date: Tue, 15 Jul 2003 13:47:34 +0100 Subject: convert a string in a sequence References: <1058272910.2646.17.camel@thym> Message-ID: <3F13F7E6.6070003@ebi.ac.uk> Carole Louis wrote: > Is it possible to convert a string in a sequence ? If it is, how can I > do it ? Yes, you can do this: AjPSeq seq; seq = ajSeqNewL(ajStrLen(str)); ajSeqAssSeq(seq, str); ... and you can expect the missing ajSeqNewStr call to appear in the next release!!! Hope this helps, Peter From gtps5 at gtptech.com Tue Jul 15 12:53:13 2003 From: gtps5 at gtptech.com (Carole Louis) Date: 15 Jul 2003 14:53:13 +0200 Subject: convert a string in a sequence In-Reply-To: <3F13F78C.B2F3B2EF@hgmp.mrc.ac.uk> References: <1058272910.2646.17.camel@thym> <3F13F78C.B2F3B2EF@hgmp.mrc.ac.uk> Message-ID: <1058273599.1425.29.camel@thym> OK. In fact, I want to use the function "ajSeqNum" where the first argument is a sequence. The problem is I don't have declare this first parameter as a sequence but as a string, at the beginnig of my program. So I want to convert the string in a sequence. It's is because I do not want to modifie all the code. Le mar 15/07/2003 ? 14:46, Dr J.C. Ison a ?crit : Carole Please provide more info. What sort of sequence? Convert the string to what? etc Cheers J. Carole Louis wrote: > Hi, > > Is it possible to convert a string in a sequence ? If it is, how can I > do it ? > > Thanks, > Carole > -- Jon C. Ison, PhD Bioinformatics Applications Group UK MRC Human Genome Mapping Project Resource Centre Hinxton, Cambridge, CB10 1SB, UK E-mail : jison at hgmp.mrc.ac.uk Tel : 01223 49-4548 HGMP-RC: http://www.hgmp.mrc.ac.uk/ EMBOSS : http://www.hgmp.mrc.ac.uk/Software/EMBOSS/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From gtps5 at gtptech.com Tue Jul 15 12:54:17 2003 From: gtps5 at gtptech.com (Carole Louis) Date: 15 Jul 2003 14:54:17 +0200 Subject: convert a string in a sequence In-Reply-To: <3F13F7E6.6070003@ebi.ac.uk> References: <1058272910.2646.17.camel@thym> <3F13F7E6.6070003@ebi.ac.uk> Message-ID: <1058273663.2646.31.camel@thym> thanks so much. Le mar 15/07/2003 ? 14:47, Peter Rice a ?crit : Carole Louis wrote: > Is it possible to convert a string in a sequence ? If it is, how can I > do it ? Yes, you can do this: AjPSeq seq; seq = ajSeqNewL(ajStrLen(str)); ajSeqAssSeq(seq, str); ... and you can expect the missing ajSeqNewStr call to appear in the next release!!! Hope this helps, Peter -------------- next part -------------- An HTML attachment was scrubbed... URL: From pmr at ebi.ac.uk Tue Jul 15 13:10:13 2003 From: pmr at ebi.ac.uk (Peter Rice) Date: Tue, 15 Jul 2003 14:10:13 +0100 Subject: convert a string in a sequence References: <1058272910.2646.17.camel@thym> <3F13F78C.B2F3B2EF@hgmp.mrc.ac.uk> <1058273599.1425.29.camel@thym> Message-ID: <3F13FD35.2070809@ebi.ac.uk> Carole Louis wrote: > In fact, I want to use the function "ajSeqNum" where the first argument > is a sequence. The problem is I don't have declare this first parameter > as a sequence but as a string, at the beginnig of my program. So I want > to convert the string in a sequence. It's is because I do not want to > modifie all the code. There will be an ajSeqNumS function in the next release that has a string as the first argument. There will also be an ajSeqNewStr function, for uses like this, but you may want to set other properties (name, accession, description) if you need the sequence so the method I posted earlier may be the simplest to use (so you can add more ajSeqAss calls). Hope this helps, Peter From gvasudevan at medarex.com Tue Jul 15 17:32:16 2003 From: gvasudevan at medarex.com (Vasudevan, Geetha) Date: Tue, 15 Jul 2003 10:32:16 -0700 Subject: clustalw question... Message-ID: <8249C3256E593D4FB066BB9998D9F7E41C9B65@ca2-fs03.ca2.2k.medarex.com> Is it possible to force the order of alignment in clustalw? I would like the first seq in the fasta file to be on top. Thanks for your help. -Geetha. -------------- next part -------------- An HTML attachment was scrubbed... URL: From kellert at ohsu.edu Tue Jul 15 17:51:00 2003 From: kellert at ohsu.edu (Thomas Keller) Date: Tue, 15 Jul 2003 10:51:00 -0700 Subject: eprimer3 warning Message-ID: Greetings, Could someone explain the following warning, and give me some advice on what to do about it? % eprimer3 tpn_r01.fa -explain -options Picks PCR primers and hybridization oligos Warning: ajStrFixI called with length 2048 for string with size 2048 .... it repeats this warning about 20 times then proceeds to give options. Thanks, Tom Keller Tom Keller, Ph.D. http://www.ohsu.edu/core kellert at ohsu.edu 503-494-2442 From fernan at iib.unsam.edu.ar Tue Jul 15 18:23:35 2003 From: fernan at iib.unsam.edu.ar (Fernan Aguero) Date: Tue, 15 Jul 2003 15:23:35 -0300 Subject: clustalw question... In-Reply-To: <8249C3256E593D4FB066BB9998D9F7E41C9B66@ca2-fs03.ca2.2k.medarex.com> References: <8249C3256E593D4FB066BB9998D9F7E41C9B66@ca2-fs03.ca2.2k.medarex.com> Message-ID: <20030715182335.GC33270@iib.unsam.edu.ar> +----[ Vasudevan, Geetha (15.Jul.2003 15:09): | | Do you know which option to use? Thanks. Most of the time i run clustalw interactively (i.e. without passing options in the command-line. In this way, I choose option 1 (sequence input), then 2 (MSA), then 9 (output format), then again 9 (toggle output order). The toggle switches between 'aligned' and 'input file'. The last one is the one you want. If you run it non-interactively you need: -OUTORDER= :INPUT or ALIGNED (output from calling 'clustalw -help') Hope this helps, Fernan | | | -----Original Message----- | From: Fernan Aguero [mailto:fernan at iib.unsam.edu.ar] | Sent: Tuesday, July 15, 2003 11:04 AM | To: Vasudevan, Geetha | Subject: Re: clustalw question... | | +----[ Vasudevan, Geetha (15.Jul.2003 14:38): | | | | Is it possible to force the order of alignment in clustalw? I would | | like the first seq in the fasta file to be on top. | | | +----] | | Yes you can. In clustalw, you can set the order of sequences | to be the same of the input file. | | Fernan | | -- | F e r n a n A g u e r o | http://genoma.unsam.edu.ar/~fernan | | +----] -- F e r n a n A g u e r o http://genoma.unsam.edu.ar/~fernan From ableasby at hgmp.mrc.ac.uk Tue Jul 15 18:46:21 2003 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Tue, 15 Jul 2003 19:46:21 +0100 (BST) Subject: eprimer3 warning Message-ID: <200307151846.h6FIkLn19654@bromine.hgmp.mrc.ac.uk> Tom, That message will appear on MacOSX if input files are used which have line lengths >=2048 characters. You need to go to the ftp://ftp.uk.embnet.org/pub/EMBOSS/patchfiles/ directory and get the 'ajsys.c' file (look at the README to see what the other replacement files are for. Just substitute the ajax/ajsys.c file with the new one, recompile/install and the problem should go away. HTH Alan From P.Ernst at dkfz-heidelberg.de Wed Jul 16 08:44:33 2003 From: P.Ernst at dkfz-heidelberg.de (Peter Ernst) Date: Wed, 16 Jul 2003 10:44:33 +0200 (MEST) Subject: acd files In-Reply-To: <3F13D366.2070400@ebi.ac.uk> Message-ID: On Tue, 15 Jul 2003, Peter Rice wrote: > Derek Gatherer wrote: > > So would that allow eg. a Perl script to be called? (I ask because I > > have many old Perl scripts of varying degrees of usefulness, but I am > > now required to provide tools within an EMBOSS-centric department). > > There was also a Perl ACD wrapper from Peter Ernst, and here at EBI we It's the CPAN Bio::Emboss module: http://www.perl.com/CPAN/modules/by-module/Bio/ Usage: for example, a perl version of the EMBOSS program 'seqret', using seqret.acd: --- snip --- use Bio::Emboss qw(:all); embInitPerl("seqret", \@ARGV); $seqall = ajAcdGetSeqall("sequence"); $seqout = ajAcdGetSeqoutall("outseq"); while ($seqall->ajSeqallNext($seq)) { $seqout->ajSeqAllWrite ($seq); } --- snip --- Regards, Peter Ernst -- ======================================================================= Peter Ernst Department of Molecular Biophysics - B020 Deutsches Krebsforschungszentrum (German Cancer Research Center) DKFZ Im Neuenheimer Feld 580 / Technologiepark 3 69120 Heidelberg, Germany phone: +49-6221-42-2330 http://genome.dkfz-heidelberg.de/ fax: +49-6221-42-2333 ======================================================================= From R-4-721447-13602970-2-13541-US2-2A4207A7 at xmr3.com Thu Jul 17 01:31:57 2003 From: R-4-721447-13602970-2-13541-US2-2A4207A7 at xmr3.com (International Scientific Communications, Inc.) Date: Wed, 16 Jul 2003 21:31:57 -0400 Subject: ISC Laboratory Technology News Message-ID: An HTML attachment was scrubbed... URL: From d.gatherer at vir.gla.ac.uk Thu Jul 17 09:53:59 2003 From: d.gatherer at vir.gla.ac.uk (Derek Gatherer) Date: Thu, 17 Jul 2003 10:53:59 +0100 Subject: wrapper for Perl scripts within EMBOSS Message-ID: <5.2.1.1.1.20030717103905.00ad8a60@udcf.gla.ac.uk> Subject: Re: acd files From: Peter Rice (pmr at ebi.ac.uk) Date: Tue 15 Jul 2003 - 11:11:50 BST >time to update the list of EMBOSS wrappers on the web pages >perhaps? I couldn't find this. Is it somewhere in a corner of the website? I have another question, which probably reveals my limited C experience, but anyway... After writing new code, I run 'make', which takes about 3 seconds. But then when I run 'make install', a period of about 7 minutes is consumed by installation of the /share/EMBOSS/data and all the acd files etc, before it gets down to the business of installing the new bin. Is there a way of turning this off, so that 'make install' just jumps to the bare necessary lib and bin installations? acdc is fine after make of course, but that only tests that the acd file is okay. Cheers Derek _________________________ Derek Gatherer Ph.D. Cert.Ed. Computer Officer Institute of Virology Church St. Glasgow G11 5JR Phone: +44 141 330 6268 Fax: +44 141 337 2236 Email: d.gatherer at vir.gla.ac.uk Website: http://www.vir.gla.ac.uk From alfons at elmeuportal.net Thu Jul 17 09:52:42 2003 From: alfons at elmeuportal.net (Alfons Nonell i Canals) Date: 17 Jul 2003 11:52:42 +0200 Subject: A simple question In-Reply-To: <5.2.1.1.1.20030717103905.00ad8a60@udcf.gla.ac.uk> References: <5.2.1.1.1.20030717103905.00ad8a60@udcf.gla.ac.uk> Message-ID: <1058435562.2527.9.camel@anxaneta> Hi! perhaps it is a offtopic question but.. I need help... One friend needs a simple program to run in Linux. She have to edit lots of sequences and, in windows, She is using BioEdit. I ask her to change to Linux but.. She needs this program! Who can tell me about a program BioEdit like for Linux? Thanks. Alfons. -------------- next part -------------- An HTML attachment was scrubbed... URL: From pmr at ebi.ac.uk Thu Jul 17 09:49:48 2003 From: pmr at ebi.ac.uk (Peter Rice) Date: Thu, 17 Jul 2003 10:49:48 +0100 Subject: wrapper for Perl scripts within EMBOSS References: <5.2.1.1.1.20030717103905.00ad8a60@udcf.gla.ac.uk> Message-ID: <3F16713C.9090107@ebi.ac.uk> Derek Gatherer wrote: > >time to update the list of EMBOSS wrappers on the web pages > >perhaps? > > I couldn't find this. Is it somewhere in a corner of the website? It's linked to the main page as "Jemboss and other Interfaces" > After writing new code, I run 'make', which takes about 3 seconds. But > then when I run 'make install', a period of about 7 minutes is consumed > by installation of the /share/EMBOSS/data and all the acd files etc, > before it gets down to the business of installing the new bin. Is there > a way of turning this off, so that 'make install' just jumps to the bare > necessary lib and bin installations? acdc is fine after make of course, > but that only tests that the acd file is okay. install and libtool have some curious interactions. With shared libraries turned off, I can do: cd emboss make myprogram cp myprogram /where/emboss/binaries/live With shared libraries on, libtool has to run scripts to do the install, and timestamp checking becomes tricky. Hope this helps. No doubt a more authoritative reply from our "make" experts will follow. Peter From gtps5 at gtptech.com Thu Jul 17 09:53:16 2003 From: gtps5 at gtptech.com (Carole Louis) Date: 17 Jul 2003 11:53:16 +0200 Subject: wrapper for Perl scripts within EMBOSS In-Reply-To: <5.2.1.1.1.20030717103905.00ad8a60@udcf.gla.ac.uk> References: <5.2.1.1.1.20030717103905.00ad8a60@udcf.gla.ac.uk> Message-ID: <1058435604.1518.26.camel@thym> Hi, I ask myself the same question :"How to do "make install" quickier ?" . Running this in the repertory "EMBOSS-2.7.1/emboss" this step takes 2 minutes. It's better than 7 minutes but not ideal. Le jeu 17/07/2003 ? 11:53, Derek Gatherer a ?crit : Subject: Re: acd files From: Peter Rice (pmr at ebi.ac.uk) Date: Tue 15 Jul 2003 - 11:11:50 BST >time to update the list of EMBOSS wrappers on the web pages >perhaps? I couldn't find this. Is it somewhere in a corner of the website? I have another question, which probably reveals my limited C experience, but anyway... After writing new code, I run 'make', which takes about 3 seconds. But then when I run 'make install', a period of about 7 minutes is consumed by installation of the /share/EMBOSS/data and all the acd files etc, before it gets down to the business of installing the new bin. Is there a way of turning this off, so that 'make install' just jumps to the bare necessary lib and bin installations? acdc is fine after make of course, but that only tests that the acd file is okay. Cheers Derek _________________________ Derek Gatherer Ph.D. Cert.Ed. Computer Officer Institute of Virology Church St. Glasgow G11 5JR Phone: +44 141 330 6268 Fax: +44 141 337 2236 Email: d.gatherer at vir.gla.ac.uk Website: http://www.vir.gla.ac.uk -------------- next part -------------- An HTML attachment was scrubbed... URL: From gtps5 at gtptech.com Thu Jul 17 10:08:25 2003 From: gtps5 at gtptech.com (Carole Louis) Date: 17 Jul 2003 12:08:25 +0200 Subject: einverted Message-ID: <1058436507.1516.39.camel@thym> Hi (again), I am trying to use the program "einverted" as a function in my own program. "einverted" would be just a part of it. So I have put "einverted" in a function (without all the steps as "embInit", ajAcd....). I have no problem to compile my program but when I try to execute it, my program do not stop. I think the problem is in the lines : for (i = 5 ; i-- ;) { AJCNEW(revmatch[i], (length+maxsave)); ip = revmatch[i]; for(j = length ; j-- ; ) *ip++ = mismatch ; for(j = maxsave ; j-- ;) *ip++ = rogue ; } When I suppress the line "AJCNEW(revmatch[i], (length+maxsave));", the execution of my program do not stop but I obtain a segmentation fault (and it is normal). Is there a special operation to do when I compile ? Thanks, Carole -------------- next part -------------- An HTML attachment was scrubbed... URL: From inagy at abc.hu Thu Jul 17 10:20:50 2003 From: inagy at abc.hu (Nagy Istvan) Date: Thu, 17 Jul 2003 12:20:50 +0200 Subject: A simple question In-Reply-To: <1058435562.2527.9.camel@anxaneta> References: <5.2.1.1.1.20030717103905.00ad8a60@udcf.gla.ac.uk> <1058435562.2527.9.camel@anxaneta> Message-ID: <20030717122050.4bb8f9ff.inagy@abc.hu> On 17 Jul 2003 11:52:42 +0200 Alfons Nonell i Canals wrote: > Who can tell me about a program BioEdit like for Linux? Besides EMBOSS and the Staden package I use GDE on Linux. GDE is nice and flexible and the best for sequence editing. Unfortunatelly it is a little bit old-fashioned and configuring it some investment of time and dedication. From d.gatherer at vir.gla.ac.uk Thu Jul 17 11:01:08 2003 From: d.gatherer at vir.gla.ac.uk (Derek Gatherer) Date: Thu, 17 Jul 2003 12:01:08 +0100 Subject: wrapper for Perl scripts within EMBOSS In-Reply-To: <3F16713C.9090107@ebi.ac.uk> References: <5.2.1.1.1.20030717103905.00ad8a60@udcf.gla.ac.uk> Message-ID: <5.2.1.1.1.20030717115926.00aaf040@udcf.gla.ac.uk> >With shared libraries turned off, I can do: Yes, this does the trick, thanks. ./configure --disable-shared just needs to be run once. Cheers Derek From mad at biol.unlp.edu.ar Thu Jul 17 12:08:39 2003 From: mad at biol.unlp.edu.ar (=?ISO-8859-1?Q?Mart=EDn_Sarachu?=) Date: Thu, 17 Jul 2003 09:08:39 -0300 Subject: EMBOSS programming course Message-ID: <3F1691C7.80804@biol.unlp.edu.ar> Hi list, anybody in here is going to the EMBOSS programming course on September? Regards, martin -- Mart?n Sarachu mad at biol.unlp.edu.ar EMBNet Argentina http://www.ar.embnet.org From d.gatherer at vir.gla.ac.uk Thu Jul 17 12:30:17 2003 From: d.gatherer at vir.gla.ac.uk (Derek Gatherer) Date: Thu, 17 Jul 2003 13:30:17 +0100 Subject: wrapper for Perl scripts within EMBOSS In-Reply-To: <3F16713C.9090107@ebi.ac.uk> References: <5.2.1.1.1.20030717103905.00ad8a60@udcf.gla.ac.uk> Message-ID: <5.2.1.1.1.20030717131011.00ac0008@udcf.gla.ac.uk> So the following would presumably be the simplest possible wrapper, just opening and running a Perl script, using a single line ACD file just to name the program and nothing else. However, the Perl script then needs to prompt for any further parameters, infiles etc. This works, but is it against the EMBOSS philosophy? I did try collecting the Perl parameters via the ACD, but didn't manage to figure out a way of easily manipulating them into the command line (ie. ajSystemEnv( &cmd, env) ). I tried things like strcat(str1, str 2) and so on, but kept running into type incompatibilities with AjPStr. Is there a standard way to push the usual collected strings from the ACD file into a concatenated string that can then act as the @ARGV for a Perl script and be called via ajSystemEnv( &cmd, env) etc? #--------------ACD file, hello.acd--------------------------------------# appl: hello [ doc: "Calls a Perl script which then does the rest of what you want to do" ] #--------------hello.c wrapper to call hello.pl-----------------------# #include "emboss.h" int main(int argc, char **argv, char **env) { AjPStr cmd=NULL; char *prog_default = "perl -w path/to/bin/hello.pl"; embInit("hello",argc,argv); // invoke the command if (!ajNamGetValueC("perl -w path/to/bin/hello.pl", &cmd)) cmd = ajStrNewC(prog_default); ajFmtError( "..%s..\n\n", ajStrStr( cmd)); ajDebug( "Executing '%S'\n", cmd); ajSystemEnv( &cmd, env); ajExit(); return 0; } From P.Ernst at dkfz-heidelberg.de Thu Jul 17 14:27:27 2003 From: P.Ernst at dkfz-heidelberg.de (Peter Ernst) Date: Thu, 17 Jul 2003 16:27:27 +0200 (MEST) Subject: wrapper for Perl scripts within EMBOSS In-Reply-To: <5.2.1.1.1.20030717131011.00ac0008@udcf.gla.ac.uk> Message-ID: On Thu, 17 Jul 2003, Derek Gatherer wrote: > So the following would presumably be the simplest possible wrapper, just > opening and running a Perl script, using a single line ACD file just to > name the program and nothing else. I think I am missing the point in this strategy. What is the advantage of having a C-Emboss wrapper around a Perl program, if you do not use any of the ACD features (eg. reading sequences)? Also, something like "-help" on the command-line will lead embInit() to dump senseless information. > However, the Perl script then needs to prompt for any further > parameters, infiles etc. Yes, because embInit() doesn't know about it. > This works, but is it against the EMBOSS philosophy? I did try > collecting the Perl parameters via the ACD, but didn't manage to > figure out a way of easily manipulating them into the command line > (ie. ajSystemEnv( &cmd, env) ). The question is here what you really want? If you don't want Emboss/ACD to interfere with your command-line, you better avoid calling embInit(). :-) However, if you want ACD to do some part of the job for you, then one has to define, what part of the work you want to leave for ACD, and what you want to do yourself in your Perl program. An example: If one of the input parameters is supposed to be an input sequence, what do you want to have? 1. The sequence as string (in what format)? 2. The filename (what to do with DB entries?) ? What to do with defaults evaluated by ACD? In fact I see 2 strategies: A.) ignore ACD B.) use ACD to work on the command-line, read in sequences, do prompting, etc... But then you have the problem to access the information ACD has collected. For exactly this purpose, there are the set of ajAcdGet....() functions in Emboss. Here is an example, how to use these functions in Perl to get the input sequence as a Perl-string from ACD: test1.acd: ---------- appl: test1 [ doc: "test1 Perl script" ] sequence: sequence [ param: "Y" req: "Y" ] test1.pl: --------- #!/usr/bin/perl # --- import all EMBOSS functions into this namespace use Bio::Emboss qw(:all); # --- store script and acd file in the same directory ($thisdir = $0) =~ s:[^/]*$::; $thisdir = "." unless length ($thisdir); $ENV{"EMBOSS_ACDROOT"} = $thisdir; embInitPerl("test1", \@ARGV); my $seqstr = ajAcdGetSeq("sequence")->ajSeqChar(); print $seqstr; usage: ------ % perl test1.pl swissprot:edd_rat test1 Perl script ARRERMTAREEASLRTLEGRRRATLLSARQGMMSARGDFLNYALSLMRSHNDEHSDVLPVLDVCSLK... or % perl test1.pl test1 Perl script Input sequence: swissprot:edd_rat ARRERMTAREEASLRTLEGRRRATLLSARQGMMSARGDFLNYALSLMRSHNDEHSDVLPVL.... and % perl test1.pl -help Mandatory qualifiers: [-sequence] sequence (no help text) sequence value Optional qualifiers: (none) Advanced qualifiers: (none) General qualifiers: -help boolean Report command line options. More information on associated and general qualifiers can be found with -help -verbose Kind regards, Peter Ernst -- ======================================================================= Peter Ernst Department of Molecular Biophysics - B020 Deutsches Krebsforschungszentrum (German Cancer Research Center) DKFZ Im Neuenheimer Feld 580 / Technologiepark 3 69120 Heidelberg, Germany phone: +49-6221-42-2330 http://genome.dkfz-heidelberg.de/ fax: +49-6221-42-2333 ======================================================================= > > #--------------ACD file, hello.acd--------------------------------------# > > appl: hello [ > doc: "Calls a Perl script which then does the rest of what you > want to do" > ] > > #--------------hello.c wrapper to call hello.pl-----------------------# > > #include "emboss.h" > > int main(int argc, char **argv, char **env) > { > AjPStr cmd=NULL; > > char *prog_default = "perl -w path/to/bin/hello.pl"; > > embInit("hello",argc,argv); > > // invoke the command > > if (!ajNamGetValueC("perl -w path/to/bin/hello.pl", &cmd)) > cmd = ajStrNewC(prog_default); > > ajFmtError( "..%s..\n\n", ajStrStr( cmd)); > ajDebug( "Executing '%S'\n", cmd); > ajSystemEnv( &cmd, env); > > ajExit(); > > return 0; > } From pmr at ebi.ac.uk Thu Jul 17 14:38:10 2003 From: pmr at ebi.ac.uk (Peter Rice) Date: Thu, 17 Jul 2003 15:38:10 +0100 Subject: wrapper for Perl scripts within EMBOSS References: Message-ID: <3F16B4D2.7020903@ebi.ac.uk> Peter Ernst wrote: > I think I am missing the point in this strategy. > > What is the advantage of having a C-Emboss wrapper around a Perl > program, if you do not use any of the ACD features (eg. reading > sequences)? It depends on how you run it. In Martin Senger's SoapLab interface, third party applications (including perl scripts) are defined by ACD files. These are used to automatically define the SOAP interface, and SoapLab handles conversion of the sequence types into something the third party application can use (Martin defines special "comment" attributes in his ACD files for this). But ... in SoapLab ACD is only used to define the interface ... SoapLab and the third party applications do not read the ACD file at run time. It would be fun, though, to be able to use ACD directly in perl. Hmmm ... I wonder ... Peter From maoj at mail.nih.gov Thu Jul 17 14:41:25 2003 From: maoj at mail.nih.gov (Jean Mao) Date: Thu, 17 Jul 2003 10:41:25 -0400 Subject: question about emboss logging Message-ID: <002201c34c71$80014c50$494de780@CIT.NIH.GOV> Hi, the default logging info contains 3 fields: program user time/date Is there a way to modify the logging system so that other info can be recorded such as CPU time, machine name etc.? Thanks. Jean -------------- next part -------------- An HTML attachment was scrubbed... URL: From pmr at ebi.ac.uk Thu Jul 17 14:43:00 2003 From: pmr at ebi.ac.uk (Peter Rice) Date: Thu, 17 Jul 2003 15:43:00 +0100 Subject: question about emboss logging References: <002201c34c71$80014c50$494de780@CIT.NIH.GOV> Message-ID: <3F16B5F4.6010602@ebi.ac.uk> Jean Mao wrote: > Hi, the default logging info contains 3 fields: program user time/date > > Is there a way to modify the logging system so that other info can be > recorded such as CPU time, machine name etc.? Thanks. It is easy to do ... Would it be useful? What information would you like? For example, we can put a header on the first record of the log file to say what information is required in each column, and log that way. Or we could make the logfile syntax more complicated - but we do not try to lock the file so there may be a few merged records in a very large file. For statistics they are not a problem. Peter From P.Ernst at dkfz-heidelberg.de Thu Jul 17 15:00:16 2003 From: P.Ernst at dkfz-heidelberg.de (Peter Ernst) Date: Thu, 17 Jul 2003 17:00:16 +0200 (MEST) Subject: wrapper for Perl scripts within EMBOSS In-Reply-To: <3F16B4D2.7020903@ebi.ac.uk> Message-ID: On Thu, 17 Jul 2003, Peter Rice wrote: > In Martin Senger's SoapLab interface, third party applications > (including perl scripts) are defined by ACD files. I think we must distinguish between the "ACD language" and the "ACD code in Emboss". Several interfaces to Emboss read files in the ACD language to build the interface to Emboss programs. However most (all?, what about Jemboss?) interfaces do not use the ACD code in Emboss to actually perform the reading. > But ... in SoapLab ACD is only used to define the interface ... SoapLab > and the third party applications do not read the ACD file at run time. > > It would be fun, though, to be able to use ACD directly in perl. This is what Perl Bio::Emboss is doing. Calling embInit() from libajax and embInit() performs all the ACD processing. Bio::Emboss just translates Perl syntax into calls to the libajax functions and back-translates some of the C data-types into Perl types. Peter Ernst From tcarver at hgmp.mrc.ac.uk Thu Jul 17 15:07:55 2003 From: tcarver at hgmp.mrc.ac.uk (Dr T. Carver) Date: Thu, 17 Jul 2003 16:07:55 +0100 (BST) Subject: wrapper for Perl scripts within EMBOSS In-Reply-To: Message-ID: > Several interfaces to Emboss read files in the ACD language to build > the interface to Emboss programs. However most (all?, what about > Jemboss?) interfaces do not use the ACD code in Emboss to actually > perform the reading. Jemboss parses the ACD files to produce the forms and calculate any inter-dependencies between parameters. From this is simply construct the command line. Tim From bgibbon at email.arizona.edu Thu Jul 17 17:10:47 2003 From: bgibbon at email.arizona.edu (Bryan Gibbon) Date: Thu, 17 Jul 2003 10:10:47 -0700 Subject: Problems compiling on MacOS X Message-ID: Hello, I am having trouble getting any recent version of EMBOSS to compile on MacOS X.2.6 (no problem for me on redhat). I am using the Dec 2002 developer tools package. I have also tried downloading and installing the most recent versions of GNU make and m4 as suggested on the EMBOSS website. The error occurs when the ajax libraries begin to be compiled but I am not familiar enough with configure/make/gcc to figure out what is going on. Below are the commands that I used to try building after the make and m4 installation and the output just prior to the error: make distclean ./configure make Making all in ajax source='ajacd.c' object='ajacd.lo' libtool=yes \ depfile='.deps/ajacd.Plo' tmpdepfile='.deps/ajacd.TPlo' \ depmode=gcc /bin/sh ../depcomp \ /bin/sh ../libtool --mode=compile gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACK AGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"EMBOSS\" -DVERSION=\"2. 7.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLI B_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES _H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DX_DISPLAY_MISSING=1 -DHAVE_DIRENT _H=1 -DSTDC_HEADERS=1 -DHAVE_UNISTD_H=1 -DGETPGRP_VOID=1 -DHAVE_STRFTIME=1 - DHAVE_UNISTD_H=1 -DHAVE_FORK=1 -DHAVE_VFORK=1 -DHAVE_WORKING_VFORK=1 -DHAVE_ WORKING_FORK=1 -DHAVE_VPRINTF=1 -DHAVE_MEMMOVE=1 -DHAVE_LIBM=1 -I. -I. -DAJ AX_FIXED_ROOT=\"/Users/bgibbon/source code/EMBOSS-2.7.1/emboss\" -DPREFIX=\"/usr/local\" -I../plplot -DNO_AUTH - g -O2 -c -o ajacd.lo `test -f 'ajacd.c' || echo './'`ajacd.c mkdir .libs gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACK AGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"EMBOSS\" -DVERSION=\"2. 7.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLI B_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES _H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DX_DISPLAY_MISSING=1 -DHAVE_DIRENT _H=1 -DSTDC_HEADERS=1 -DHAVE_UNISTD_H=1 -DGETPGRP_VOID=1 -DHAVE_STRFTIME=1 - DHAVE_UNISTD_H=1 -DHAVE_FORK=1 -DHAVE_VFORK=1 -DHAVE_WORKING_VFORK=1 -DHAVE_ WORKING_FORK=1 -DHAVE_VPRINTF=1 -DHAVE_MEMMOVE=1 -DHAVE_LIBM=1 -I. -I. -DAJA X_FIXED_ROOT=\"/Users/bgibbon/source code/EMBOSS-2.7.1/emboss\" -DPREFIX=\"/usr/local\" -I../plplot -DNO_AUTH -g -O2 -c ajacd.c -Wp,-MD,.deps/ajacd.TPlo -fno-common -DPIC -o .libs/ajacd.o gcc: cannot specify -o with -c or -S and multiple compilations make[1]: *** [ajacd.lo] Error 1 make: *** [all-recursive] Error 1 Bryan Gibbon Department of Plant Sciences University of Arizona Tucson, AZ 85721 Phone- 520-621-9154 Fax- 520-621-3692 http://ag.arizona.edu/research/larkinslab/members/gibbon.htm From kvddrift at earthlink.net Thu Jul 17 21:51:18 2003 From: kvddrift at earthlink.net (Koen van der Drift) Date: Thu, 17 Jul 2003 17:51:18 -0400 Subject: Problems compiling on MacOS X In-Reply-To: Message-ID: On Thursday, July 17, 2003, at 01:10 PM, Bryan Gibbon wrote: > Hello, > I am having trouble getting any recent version of EMBOSS to compile on > MacOS > X.2.6 (no problem for me on redhat). I am using the Dec 2002 developer > tools > package. I have also tried downloading and installing the most recent > versions of GNU make and m4 as suggested on the EMBOSS website. Bryan, Try installing EMBOSS through the fink system (fink.sf.net). After installing fink, just type 'fink install emboss'. This will take care of downloading, compiling, and installing all necessary packages. Note that from a fresh fink EMBOSS 2.6.0 will be installed. Version 2.7.1 is available, but only as a so-called 'unstable' package. See the fink docs how to enable the unstable packages. After that, again type 'fink install emboss'. Good luck, - Koen. From kellert at ohsu.edu Thu Jul 17 22:11:04 2003 From: kellert at ohsu.edu (Thomas Keller) Date: Thu, 17 Jul 2003 15:11:04 -0700 Subject: Problems compiling on MacOS X In-Reply-To: Message-ID: <8E843979-B8A3-11D7-86E5-0003930405E2@ohsu.edu> Bill Van Etten at the BioTeam has put together some installers for Mac OS X. He's down one for emboss-2.5.1. I've used them and they've worked well. You can download from http://bioteam.net/MacOSX/biotools-1/ Good luck, Tom Keller On Thursday, July 17, 2003, at 10:10 AM, Bryan Gibbon wrote: > Hello, > I am having trouble getting any recent version of EMBOSS to compile on > MacOS > X.2.6 (no problem for me on redhat). I am using the Dec 2002 developer > tools > package. I have also tried downloading and installing the most recent > versions of GNU make and m4 as suggested on the EMBOSS website. The > error > occurs when the ajax libraries begin to be compiled but I am not > familiar > enough with configure/make/gcc to figure out what is going on. Below > are the > commands that I used to try building after the make and m4 > installation and > the output just prior to the error: > > make distclean > ./configure > make > > Making all in ajax > source='ajacd.c' object='ajacd.lo' libtool=yes \ > depfile='.deps/ajacd.Plo' tmpdepfile='.deps/ajacd.TPlo' \ > depmode=gcc /bin/sh ../depcomp \ > /bin/sh ../libtool --mode=compile > gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" > -DPACK > AGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"EMBOSS\" > -DVERSION=\"2. > 7.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 > -DHAVE_STDLI > B_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 > -DHAVE_INTTYPES > _H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DX_DISPLAY_MISSING=1 > -DHAVE_DIRENT > _H=1 -DSTDC_HEADERS=1 -DHAVE_UNISTD_H=1 -DGETPGRP_VOID=1 > -DHAVE_STRFTIME=1 - > DHAVE_UNISTD_H=1 -DHAVE_FORK=1 -DHAVE_VFORK=1 -DHAVE_WORKING_VFORK=1 > -DHAVE_ > WORKING_FORK=1 -DHAVE_VPRINTF=1 -DHAVE_MEMMOVE=1 -DHAVE_LIBM=1 -I. > -I. -DAJ > AX_FIXED_ROOT=\"/Users/bgibbon/source > code/EMBOSS-2.7.1/emboss\" -DPREFIX=\"/usr/local\" -I../plplot > -DNO_AUTH - > g -O2 -c -o ajacd.lo `test -f 'ajacd.c' || echo './'`ajacd.c > mkdir .libs > > gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" > -DPACK > AGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"EMBOSS\" > -DVERSION=\"2. > 7.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 > -DHAVE_STDLI > B_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 > -DHAVE_INTTYPES > _H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DX_DISPLAY_MISSING=1 > -DHAVE_DIRENT > _H=1 -DSTDC_HEADERS=1 -DHAVE_UNISTD_H=1 -DGETPGRP_VOID=1 > -DHAVE_STRFTIME=1 - > DHAVE_UNISTD_H=1 -DHAVE_FORK=1 -DHAVE_VFORK=1 -DHAVE_WORKING_VFORK=1 > -DHAVE_ > WORKING_FORK=1 -DHAVE_VPRINTF=1 -DHAVE_MEMMOVE=1 -DHAVE_LIBM=1 -I. -I. > -DAJA > X_FIXED_ROOT=\"/Users/bgibbon/source > code/EMBOSS-2.7.1/emboss\" -DPREFIX=\"/usr/local\" -I../plplot > -DNO_AUTH -g > -O2 -c ajacd.c -Wp,-MD,.deps/ajacd.TPlo -fno-common -DPIC -o > .libs/ajacd.o > gcc: cannot specify -o with -c or -S and multiple compilations > make[1]: *** [ajacd.lo] Error 1 > make: *** [all-recursive] Error 1 > > Bryan Gibbon > Department of Plant Sciences > University of Arizona > Tucson, AZ 85721 > > Phone- 520-621-9154 > Fax- 520-621-3692 > > http://ag.arizona.edu/research/larkinslab/members/gibbon.htm > > From mbb8n at virginia.edu Fri Jul 18 00:34:46 2003 From: mbb8n at virginia.edu (Michael Black) Date: Thu, 17 Jul 2003 20:34:46 -0400 Subject: Problems compiling on MacOS X Message-ID: <7538FDE0-B8BF-11D7-95E4-0003931D9E4A@virginia.edu> Sorry I can't offer any specific answer, and I have read the responses you've received. I can say that I have installed EMBOSS 2.7.1 on two Apple OS X machines without any problems. These were a TiBook and DP 1.25 PowerMac, both running 10.2.6, with the Dec. 2002 developers tools, but with the gcc 3.3 patch applied. The libajax installed fine. I do not like installing EMBOSS via FINK (which I do use for other installs), since I want the control of a stand alone install (in /usr/local/bin, with png support), and I use the standalone version of JemBoss (which also installed fine). All I can suggest is manually removing any previous EMBOSS libs, and trying the install again - from my experience it should work flawlessly, but I did completely blow away my previous 2.6.0 installs before installing 2.7.1. Oh, and I did use FINK to install libpng and gd, but that has worked fine for me since at least EMBOSS 2.5 Best of luck, Michael ____________________________________________ Michael B. Black, Ph.D. Molecular Biology Computing Support ITC-ACHS, Univ. of Virginia ____________________________________________ On Thursday, July 17, 2003, at 01:10 PM, Bryan Gibbon wrote: > Hello, > I am having trouble getting any recent version of EMBOSS to compile on > MacOS > X.2.6 (no problem for me on redhat). I am using the Dec 2002 developer > tools > package. I have also tried downloading and installing the most recent > versions of GNU make and m4 as suggested on the EMBOSS website. The > error > occurs when the ajax libraries begin to be compiled but I am not > familiar > enough with configure/make/gcc to figure out what is going on. Below > are the > commands that I used to try building after the make and m4 > installation and > the output just prior to the error: > > make distclean > ./configure > make > > Making all in ajax > source='ajacd.c' object='ajacd.lo' libtool=yes \ > depfile='.deps/ajacd.Plo' tmpdepfile='.deps/ajacd.TPlo' \ > depmode=gcc /bin/sh ../depcomp \ > /bin/sh ../libtool --mode=compile > gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" > -DPACK > AGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"EMBOSS\" > -DVERSION=\"2. > 7.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 > -DHAVE_STDLI > B_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 > -DHAVE_INTTYPES > _H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DX_DISPLAY_MISSING=1 > -DHAVE_DIRENT > _H=1 -DSTDC_HEADERS=1 -DHAVE_UNISTD_H=1 -DGETPGRP_VOID=1 > -DHAVE_STRFTIME=1 - > DHAVE_UNISTD_H=1 -DHAVE_FORK=1 -DHAVE_VFORK=1 -DHAVE_WORKING_VFORK=1 > -DHAVE_ > WORKING_FORK=1 -DHAVE_VPRINTF=1 -DHAVE_MEMMOVE=1 -DHAVE_LIBM=1 -I. > -I. -DAJ > AX_FIXED_ROOT=\"/Users/bgibbon/source > code/EMBOSS-2.7.1/emboss\" -DPREFIX=\"/usr/local\" -I../plplot > -DNO_AUTH - > g -O2 -c -o ajacd.lo `test -f 'ajacd.c' || echo './'`ajacd.c > mkdir .libs > > gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" > -DPACK > AGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"EMBOSS\" > -DVERSION=\"2. > 7.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 > -DHAVE_STDLI > B_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 > -DHAVE_INTTYPES > _H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DX_DISPLAY_MISSING=1 > -DHAVE_DIRENT > _H=1 -DSTDC_HEADERS=1 -DHAVE_UNISTD_H=1 -DGETPGRP_VOID=1 > -DHAVE_STRFTIME=1 - > DHAVE_UNISTD_H=1 -DHAVE_FORK=1 -DHAVE_VFORK=1 -DHAVE_WORKING_VFORK=1 > -DHAVE_ > WORKING_FORK=1 -DHAVE_VPRINTF=1 -DHAVE_MEMMOVE=1 -DHAVE_LIBM=1 -I. -I. > -DAJA > X_FIXED_ROOT=\"/Users/bgibbon/source > code/EMBOSS-2.7.1/emboss\" -DPREFIX=\"/usr/local\" -I../plplot > -DNO_AUTH -g > -O2 -c ajacd.c -Wp,-MD,.deps/ajacd.TPlo -fno-common -DPIC -o > .libs/ajacd.o > gcc: cannot specify -o with -c or -S and multiple compilations > make[1]: *** [ajacd.lo] Error 1 > make: *** [all-recursive] Error 1 > > Bryan Gibbon > Department of Plant Sciences > University of Arizona > Tucson, AZ 85721 > > Phone- 520-621-9154 > Fax- 520-621-3692 > > http://ag.arizona.edu/research/larkinslab/members/gibbon.htm > > From d.gatherer at vir.gla.ac.uk Fri Jul 18 08:42:38 2003 From: d.gatherer at vir.gla.ac.uk (Derek Gatherer) Date: Fri, 18 Jul 2003 09:42:38 +0100 Subject: wrapper for Perl scripts within EMBOSS In-Reply-To: References: <5.2.1.1.1.20030717131011.00ac0008@udcf.gla.ac.uk> Message-ID: <5.2.1.1.1.20030718093617.00a9bcc8@udcf.gla.ac.uk> At 16:27 17/07/2003 +0200, Peter Ernst wrote: > use Bio::Emboss qw(:all); Yes, thanks, this appears to be what I'm looking for. Just for clarification, Bio::EMBOSS http://search.cpan.org/author/PERNST/Bio-Emboss-0.3/Emboss.pm does not require BioPerl, unlike Bio::Factory::EMBOSS http://doc.bioperl.org/releases/bioperl-1.2/Bio/Factory/EMBOSS.html ??? Cheers Derek From bgibbon at email.arizona.edu Sun Jul 20 16:40:35 2003 From: bgibbon at email.arizona.edu (Bryan Gibbon) Date: Sun, 20 Jul 2003 09:40:35 -0700 Subject: Problems compiling on MacOS X In-Reply-To: Message-ID: Hello, Thanks for the prompt responses to my question. It turns out that the problem was with either the capital "S" or the space in by directory named "Source code". EMBOSS built without a problem when I changed the directory name to "src". I need to remember to stick to Unix conventions when working at the command line in OS X! Bryan Gibbon From Peter.Robinson at t-online.de Sun Jul 20 19:16:12 2003 From: Peter.Robinson at t-online.de (peter robinson) Date: Sun, 20 Jul 2003 21:16:12 +0200 Subject: vector vs AjPInt2D Message-ID: <200307202116.12103.peter.robinson@t-online.de> Dear EMBOSSers, from perusal of SRS I take it that AjPInt2D is intended to be something like C++'s vector. I would like to use this for a new CpG program in order to store locations of C, G, CG in order to avoid repeatedly scanning the input sequence (I will probably try some sort of buffer to avoid blowing up the space requirements too much). I was wondering if anyone could point me to a good example of using AjPInt2D for this purpose? Thanks Peter From f.jossinet at ibmc.u-strasbg.fr Mon Jul 21 10:09:13 2003 From: f.jossinet at ibmc.u-strasbg.fr (Fabrice Jossinet) Date: Mon, 21 Jul 2003 12:09:13 +0200 Subject: take care about GU pairs in RNA sequences Message-ID: <200307211209.13666.f.jossinet@ibmc.u-strasbg.fr> Hi all, EMBOSS applications are very nice for nucleotides sequences analyses. But if the sequence is an RNA one, allowing GU/GT base pairs is not an available option. Does somebody try something to resolve that ? Thank you, Fabrice J -- ------------------------------------------------------------------------ Dr. Fabrice Jossinet Institut de biologie moleculaire et cellulaire, UPR9002, CNRS Universite Louis Pasteur 15 rue Rene Descartes F-67084 Strasbourg Cedex France Tel + 33 (0) 3 88 417044 FAX + 33 (0) 3 88 417066 or + 33 (0) 3 60 22 18 (long faxes) f.jossinet at ibmc.u-strasbg.fr http://www.fjossi.net/ http://www-ibmc.u-strasbg.fr/upr9002/westhof/ ------------------------------------------------------------------------ From rcalma at mondenet.com Tue Jul 22 20:06:16 2003 From: rcalma at mondenet.com (Canada Books) Date: Tue, 22 Jul 2003 16:06:16 -0400 Subject: Federal provincial funds Message-ID: <20030722200529.41F857D21F@mercury.hgmp.mrc.ac.uk> CANADA BOOKS 36 Felix Renaud Aylmer Qc J9H 7C1 (819)682-7983 PRESS RELEASE CANADIAN SUBSIDY DIRECTORY YEAR 2003 EDITION Legal Deposit-National Library of Canada ISBN 2-922870-05-7 The new revised edition of the Canadian Subsidy Directory 2003 is now available. 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Assistance from and for foundations and associations, guidance to prepare a business plan, market surveys, computers, and much more! The Canadian Subsidy Directory is sold $ 69.95, to obtain a copy please call: Canada Books, (819)682-7983 or Canadian business resource center (250)381-4822 From yoskim at NMSU.Edu Wed Jul 23 22:17:49 2003 From: yoskim at NMSU.Edu (Yosep) Date: Wed, 23 Jul 2003 16:17:49 -0600 (MDT) Subject: Runtime error... Message-ID: Hello! I have finally & succesfully instally Jemboss on my NetBSD machine, meaning I didn't get any installing error. Now, I followed the online help for setting up the environment variables and so on for the Standalone Mode. However, I get this error message when I run the "runJemboss.csh" script. yosep at typha: {599} ./runJemboss.csh [1] 6526 yosep at typha: {600} Standalone mode Font specified in font.properties not found [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] Font specified in font.properties not found [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] Font specified in font.properties not found [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] Font specified in font.properties not found [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] Font specified in font.properties not found [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] Font specified in font.properties not found [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] Font specified in font.properties not found [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] Font specified in font.properties not found [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] Font specified in font.properties not found [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] Font specified in font.properties not found [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] Font specified in font.properties not found [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] Font specified in font.properties not found [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] Font specified in font.properties not found [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] Font specified in font.properties not found [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] Font specified in font.properties not found [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] Font specified in font.properties not found [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] Font specified in font.properties not found [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] Font specified in font.properties not found [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] Font specified in font.properties not found [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] Font specified in font.properties not found [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] /packages/emboss/STABLE/bin/wossname -colon -auto RunEmbossApplication Error executing: /packages/emboss/STABLE/bin/wossname -colon -auto java.lang.NullPointerException at org.emboss.jemboss.programs.RunEmbossApplication.isProcessStdout(RunEmbossApplication.java:71) at org.emboss.jemboss.gui.BuildProgramMenu$1.construct(BuildProgramMenu.java:231) at org.emboss.jemboss.gui.SwingWorker$2.run(SwingWorker.java:127) at java.lang.Thread.run(Thread.java:479) How can I fix these errors? Any help would be greatly appreciated. ============= |\/\/| | Yosep Kim |,,,,| | NMSU Computer Lab Assistant | | | Computer Science, B.S. [|^ ^|] | New Mexico State Unversity \__/ | http://web.nmsu.edu/~yoskim ============= PHIL 4:13 From tcarver at hgmp.mrc.ac.uk Thu Jul 24 06:11:46 2003 From: tcarver at hgmp.mrc.ac.uk (Dr T. Carver) Date: Thu, 24 Jul 2003 07:11:46 +0100 (BST) Subject: Runtime error... In-Reply-To: Message-ID: Hi Yosep These errors look like you may not have used the install script provided (EMBOSS-2.7.1/jemboss/utils/install-jemboss-server.sh) with a fresh download of EMBOSS-2.7.1. This should have changed the values in $EMBOSS_INSTALL/share/EMBOSS/jemboss/resources/jemboss.properties to reflect the directory structure for your installation. If you did not use the install script, I recommend you try using that. If you did then you can try editing: $EMBOSS_INSTALL/share/EMBOSS/jemboss/resources/jemboss.properties and look at the description of the variables at: http://www.hgmp.mrc.ac.uk/Software/EMBOSS/Jemboss/install/properties.html Hope this helps. Regards Tim Carver HGMP-RC On Wed, 23 Jul 2003, Yosep wrote: > > Hello! > > I have finally & succesfully instally Jemboss on my NetBSD machine, > meaning I didn't get any installing error. Now, I followed the online > help for setting up the environment variables and so on for the Standalone > Mode. However, I get this error message when I run the "runJemboss.csh" > script. > > yosep at typha: {599} ./runJemboss.csh > [1] 6526 > yosep at typha: {600} Standalone mode > Font specified in font.properties not found > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] > Font specified in font.properties not found > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] > Font specified in font.properties not found > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] > Font specified in font.properties not found > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] > Font specified in font.properties not found > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] > Font specified in font.properties not found > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] > Font specified in font.properties not found > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] > Font specified in font.properties not found > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] > Font specified in font.properties not found > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] > Font specified in font.properties not found > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] > Font specified in font.properties not found > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] > Font specified in font.properties not found > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] > Font specified in font.properties not found > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] > Font specified in font.properties not found > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] > Font specified in font.properties not found > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] > Font specified in font.properties not found > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] > Font specified in font.properties not found > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] > Font specified in font.properties not found > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] > Font specified in font.properties not found > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] > Font specified in font.properties not found > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] > /packages/emboss/STABLE/bin/wossname -colon -auto > RunEmbossApplication Error executing: /packages/emboss/STABLE/bin/wossname -colon -auto > java.lang.NullPointerException > at org.emboss.jemboss.programs.RunEmbossApplication.isProcessStdout(RunEmbossApplication.java:71) > at org.emboss.jemboss.gui.BuildProgramMenu$1.construct(BuildProgramMenu.java:231) > at org.emboss.jemboss.gui.SwingWorker$2.run(SwingWorker.java:127) > at java.lang.Thread.run(Thread.java:479) > > How can I fix these errors? > Any help would be greatly appreciated. > > > ============= > |\/\/| | Yosep Kim > |,,,,| | NMSU Computer Lab Assistant > | | | Computer Science, B.S. > [|^ ^|] | New Mexico State Unversity > \__/ | http://web.nmsu.edu/~yoskim > ============= > PHIL 4:13 > From gwilliam at hgmp.mrc.ac.uk Thu Jul 24 14:55:40 2003 From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522) Date: Thu, 24 Jul 2003 15:55:40 +0100 Subject: Do you have an interface to EMBOSS? Message-ID: <3F1FF36C.CE33B7E5@hgmp.mrc.ac.uk> We would like to update our web page http://www.hgmp.mrc.ac.uk/Software/EMBOSS/interfaces.html describing the details of interfaces that people have developed for EMBOSS. If you have an interface that is not described on this page, or if you have an interface that could be described better, please reply to me or this mailing list. Many thanks, Gary -- Gary Williams Tel: +44 1223 494522 Fax: +44 1223 494512 mailto:G.Williams at hgmp.mrc.ac.uk http://www.hgmp.mrc.ac.uk/ Bioinformatics, MRC HGMP, Hinxton, Cambridge, CB10 1SB, UK From alfons at elmeuportal.net Fri Jul 25 10:24:08 2003 From: alfons at elmeuportal.net (Alfons Nonell i Canals) Date: 25 Jul 2003 12:24:08 +0200 Subject: Consed users. Message-ID: <1059128648.2521.30.camel@anxaneta> Hi! I know that is, perhaps, an oftopic message but,I need help and some of you can told me how to resolve a little problem. I'm a young student that is using phred-phra-consed to assembly lots of seq?ences. One day, when I added new reads to my assembly, in the bash terminal appeared an error like it: 1: Can't figure out read type for 1_S2APIII_A02_S2APIII_1.b.ab1.phd.1 since after the underscore is S2APIII_A02_S2APIII_1 1: Can't figure out read type for 1_S2APIII_A03_S2APIII_1.b.ab1.phd.1 since after the underscore is S2APIII_A03_S2APIII_1 After that, I updated my consed (v12) to the latest version, 13 but... the problem didn't disapear... I've studiet all perl scripts of the package and I've discovered a line in determineReadtypes.perl with that errror but.. I don't know the meaning of it. Somebody can help me? I need that programs to my job research... Thanks. Alfons. Departament de Gen?tica i microbiologia. Universitat Aut?noma de Barcelona -------------- next part -------------- An HTML attachment was scrubbed... URL: From amitsharma at movemail.com Fri Jul 25 14:09:36 2003 From: amitsharma at movemail.com (AMIT sharma) Date: Fri, 25 Jul 2003 22:09:36 +0800 Subject: back translate software developmet Message-ID: <20030725140936.14701.qmail@movemail.com> sir , I'm a student of National Institute of tech. and currenly working under Er. Mr Amit Nargotra (Engineer Bioinformatics Division of CSIR's RRL lab" we are trying to back translate the protien sequence to its nucleotide sequence using Codon Biasing. we are trying to make it platefom independent utility which just require JRE . we have completed the initial step and our program is able to produce all possible combinations pertaining to the protien chain(for it we have use the Dynamic progamming as well as Backtracking) but we are stuck to Reduce the Solution set to find an optimum number of parent sequences because of the lack of knoledge about codon baising criteria.We will be highly indept and gratified if you kindly help us out. Amit sharma Amit Nargotra -- _______________________________________________ Get your free email from http://www.movemail.com Powered by Outblaze From newgene at bigfoot.com Tue Jul 29 14:15:10 2003 From: newgene at bigfoot.com (Chunlei Wu) Date: Tue, 29 Jul 2003 09:15:10 -0500 Subject: [EMBOSS]xwindows output problem under solaris Message-ID: <3F26816E.8010702@bigfoot.com> Hi, group, I just installed latest EMBOSS v2.7.1 on my solaris 9 box. Everything seems OK except that I cannot use xwindows or X11 as my graph output. It complains that "Error in XCreatePixmap: BadDrawable (invalid Pixmap or Window parameter)." What is the problem here? I hope you can help me out. Thank you in advance. BTW: A suggestion, can this mailing list be flaged by "[EMBOSS]" at the title of all post, like the title of this email? Many of mailing list have this feature. It will be helpful for organizing incoming emails. Chunlei From David.Bauer at SCHERING.DE Tue Jul 29 14:43:55 2003 From: David.Bauer at SCHERING.DE (David.Bauer at SCHERING.DE) Date: Tue, 29 Jul 2003 16:43:55 +0200 Subject: Antwort: [EMBOSS]xwindows output problem under solaris Message-ID: Hi, this sounds like you are using Hummingbird Exceed. Go to Xconfig -> Screen Definition and set "Server Visual" to "Pseudocolor". Cheers, David. Chunlei Wu An: emboss at embnet.org Gesendet von: Kopie: owner-emboss at hgm Thema: [EMBOSS]xwindows output problem under solaris p.mrc.ac.uk 29.07.03 16:15 Hi, group, I just installed latest EMBOSS v2.7.1 on my solaris 9 box. Everything seems OK except that I cannot use xwindows or X11 as my graph output. It complains that "Error in XCreatePixmap: BadDrawable (invalid Pixmap or Window parameter)." What is the problem here? I hope you can help me out. Thank you in advance. BTW: A suggestion, can this mailing list be flaged by "[EMBOSS]" at the title of all post, like the title of this email? Many of mailing list have this feature. It will be helpful for organizing incoming emails. Chunlei From asen.nenov at metalife.de Wed Jul 30 07:31:06 2003 From: asen.nenov at metalife.de (Asen Nenov) Date: Wed, 30 Jul 2003 10:31:06 +0300 Subject: [EMBOSS] Emboss Windows vs. Linus running time comparison Message-ID: <3F27743A.6000605@metalife.de> Hello to all, I have a task to provide information on "Which OS to use if I want to run EMBOSS rapidly?". I know the original (under Linux) must be the best optimized, but this question has to be answered. A comparisom is a must. Anyone who have done this before? Any ideas of a test set or an option to use? Thanks Asen METALIFE.de From sebastian.bassi at ar.advantaseeds.com Wed Jul 30 15:35:08 2003 From: sebastian.bassi at ar.advantaseeds.com (Bassi, Sebastian) Date: Wed, 30 Jul 2003 17:35:08 +0200 Subject: [EMBOSS] RE: Do you have an interface to EMBOSS? Message-ID: Hi, I've just wrote a web interface to AbiView. It's written in Python. I'm sending them as an attach (the HTML were the input data form is and the cgi where the python program is coded). Sebastian Bassi. Advanta Seeds. Balcarce Research Station. > -----Original Message----- > From: Gary Williams, Tel 01223 494522 [mailto:gwilliam at hgmp.mrc.ac.uk] > Sent: Thursday, July 24, 2003 11:56 AM > To: emboss at embnet.org > Subject: Do you have an interface to EMBOSS? > > > We would like to update our web page > http://www.hgmp.mrc.ac.uk/Software/EMBOSS/interfaces.html > describing the details of interfaces that people have developed for > EMBOSS. > > If you have an interface that is not described on this page, or if you > have an interface that could be described better, please > reply to me or > this mailing list. > > Many thanks, > Gary > > > -- > Gary Williams Tel: +44 1223 494522 Fax: +44 1223 494512 > mailto:G.Williams at hgmp.mrc.ac.uk http://www.hgmp.mrc.ac.uk/ > Bioinformatics, MRC HGMP, Hinxton, Cambridge, CB10 1SB, UK > -------------- next part -------------- A non-text attachment was scrubbed... Name: abiview.cgi Type: application/octet-stream Size: 2463 bytes Desc: abiview.cgi URL: -------------- next part -------------- An HTML attachment was scrubbed... URL: From sebastian.bassi at ar.advantaseeds.com Wed Jul 30 15:35:17 2003 From: sebastian.bassi at ar.advantaseeds.com (Bassi, Sebastian) Date: Wed, 30 Jul 2003 17:35:17 +0200 Subject: [EMBOSS] AbiView color change suggested Message-ID: Hi, As I note in the previous mail, I've been working in a GUI for ABIVIEW. I found a little problem the the output of abiview. The colors choosen for the bases are not the standard that ABI uses. We have 2 ABIs machines: 310 and 3100, in both of them the default color code is: A=GREEN C=BLUE T=RED G=BLACK (or yellow using black background). I also have the book "Bioinformatics Sequence and Genome Analysis" by David Mount (*) and there is an ABI output sample at page 21, where the color code I stated above is used. Sequence from a third party sequencer team gave us an eletrogram with those color also. But the abiview output are in different color. Here is the color code for abiview: A=GREEN C=RED T=BLACK G=BLUE For me this is not a problem, since I work with the text file, but people on the wetlab are used to the ABI original color codes. As their request, I modified the source code of ABIVIEW to reflect color code. Here is the relevant line: return ((B)=='C'?RED:(B)=='A'?GREEN:(B)=='G'?BLUE:(B)=='T'?BLACK:YELLOW); this was changed to: return ((B)=='T'?RED:(B)=='A'?GREEN:(B)=='C'?BLUE:(B)=='G'?BLACK:YELLOW); The question/request are: 1- Could this change make into the main tree? 2- Another option would be to include a command line option to change the colors. If the color are somehow related with the dye used, color could change from run to run. So a parameter to change it would be nice. 3- There should be an option for a "silence" mode, I mean, no output to stdout (just write the files), this would help on scritping. Now the program is sending to stdout the names of the files is generates (at least is doing this when is writing pngs files). Sebastian Bassi. Advanta Seeds. Balcarce Research Station. From jrvalverde at cnb.uam.es Thu Jul 31 06:39:17 2003 From: jrvalverde at cnb.uam.es (=?ISO-8859-15?Q?Jos=E9?= R. Valverde) Date: Thu, 31 Jul 2003 08:39:17 +0200 Subject: [EMBOSS] AbiView color change suggested In-Reply-To: References: Message-ID: <20030731083917.1ce5c17c.jrvalverde@cnb.uam.es> On Wed, 30 Jul 2003 17:35:17 +0200 "Bassi, Sebastian" wrote: > 2- Another option would be to include a command line option to change the colors. If the color are somehow related with the dye used, color could change from run to run. So a parameter to change it would be nice. That would be a really good idea. Many people are blind to colours (about 2%, which is a lot) and giving them a choice is a Good Thing. j From tcarver at hgmp.mrc.ac.uk Thu Jul 31 07:24:04 2003 From: tcarver at hgmp.mrc.ac.uk (Dr T. Carver) Date: Thu, 31 Jul 2003 08:24:04 +0100 (BST) Subject: [EMBOSS] AbiView color change suggested In-Reply-To: <20030731083917.1ce5c17c.jrvalverde@cnb.uam.es> Message-ID: I agree that providing an extra option would be the best way of doing this. I will get round to looking at doing that soon. Tim On Thu, 31 Jul 2003, [ISO-8859-15] Jos? R. Valverde wrote: > On Wed, 30 Jul 2003 17:35:17 +0200 > "Bassi, Sebastian" wrote: > > 2- Another option would be to include a command line option to change the colors. If the color are somehow related with the dye used, color could change from run to run. So a parameter to change it would be nice. > > That would be a really good idea. Many people are blind to colours > (about 2%, which is a lot) and giving them a choice is a Good Thing. > > j >