From uludag at ebi.ac.uk Thu May 1 12:23:09 2008 From: uludag at ebi.ac.uk (Mahmut Uludag) Date: Thu, 01 May 2008 17:23:09 +0100 Subject: [EMBOSS] Help/Info in Jemboss In-Reply-To: References: Message-ID: <1209658990.14653.90.camel@emboss2.ebi.ac.uk> > When on goes to run an EMBOSS program from Jemboss, there is a little dark > blue icon with an ?i? in it. Clicking on this produces this message: > > A real web site is > http://emboss.sourceforge.net/apps/release/4.0/emboss/apps/seqret.html > BUT the URL in the window has a tandem duplication of ?apps/? > > How can this be ameliorated? > > The part up thru the first apps is embossURL in jemboss.resources. > Should this be truncated? Yes. The URL should also point to release 5.0. I will fix the extra "apps" bit and will find a way to avoid URLs with wrong version numbers in future releases. Regards, Mahmut From ajb at ebi.ac.uk Mon May 5 12:33:48 2008 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Mon, 5 May 2008 17:33:48 +0100 (BST) Subject: [EMBOSS] [Fwd: BOSC 2008 Announcement and Call For Submissions] Message-ID: <34936.86.14.232.77.1210005228.squirrel@webmail.ebi.ac.uk> ---------------------------- Original Message ---------------------------- Subject: BOSC 2008 Announcement and Call For Submissions From: darin.london at duke.edu Date: Mon, May 5, 2008 3:08 pm To: emboss-owner at lists.open-bio.org -------------------------------------------------------------------------- BOSC 2008 Call for Abstracts Reminder The 9th annual Bioinformatics Open Source Conference (BOSC 2008) will take place in Toronto, Ontario, Canada, as one of several Special Interest Group (SIG) meetings occurring in conjunction with the 16th annual Intelligent Systems for Molecular Biology Conference (ISMB 2008). This is the final reminder to submit your proposals for talks to the BOSC submission system before May 11. Submission Process: All abstracts must be submitted through our Open Conference Systems site (http://events.open-bio.org/BOSC2008/openconf.php). The form will ask for a small Abstract Text to be pasted into it, and a full paper. The small Abstract text should be a summary, while the longer abstract (should provide more details, including the open-source license requirement details) Full-length abstracts are limited to one page with one inch (2.5 cm) margins on the top, sides, and bottom. The full-length abstract should include the title, authors, and affiliations. We prefer your abstract to be in PDF format, although plain t Important Dates: May 11: Abstract submission deadline. June 2: Notification of accepted talks. June 4: Early registration discount cut-off. July 18-19: BOSC 2008! We hope to see you at BOSC 2008! Kam Dahlquist and Darin London BOSC 2008 Co-organizers From Marc.Logghe at ablynx.com Wed May 14 04:14:29 2008 From: Marc.Logghe at ablynx.com (Marc Logghe) Date: Wed, 14 May 2008 10:14:29 +0200 Subject: [EMBOSS] transeq feature/bug Message-ID: <03C512635899144083CADB0EE222018901AB14E3@alpaca.lan.ablynx.com> Hi all, A Pise user reported the following issue when running transeq: the resulting translation is dependant on the order of the input sequences. As it seems, transeq takes the length of the first sequence and uses that range to translate. Which is fine, but that range is used as well for all the sequences that are coming after, which is wrong. If it happens that your first sequence in the list is smaller than the ones coming after, then all translations are truncated. I think that is a bug. Embossversion 5.0.0. Regards, Marc From pmr at ebi.ac.uk Wed May 14 05:53:38 2008 From: pmr at ebi.ac.uk (Peter Rice) Date: Wed, 14 May 2008 10:53:38 +0100 Subject: [EMBOSS] transeq feature/bug In-Reply-To: <03C512635899144083CADB0EE222018901AB14E3@alpaca.lan.ablynx.com> References: <03C512635899144083CADB0EE222018901AB14E3@alpaca.lan.ablynx.com> Message-ID: <482AB6A2.3070807@ebi.ac.uk> Marc Logghe wrote: > Hi all, > > A Pise user reported the following issue when running transeq: the > resulting translation is dependant on the order of the input sequences. > > As it seems, transeq takes the length of the first sequence and uses > that range to translate. Which is fine, but that range is used as well > for all the sequences that are coming after, which is wrong. > > If it happens that your first sequence in the list is smaller than the > ones coming after, then all translations are truncated. > > I think that is a bug. Strange - we have QA tests for exactly those cases and they are working in releases 5.0.0 and earlier releases. Ah, but perhaps this is a Pise problem. If Pise is putting -send on the command line with the length of the first sequence, then this will make EMBOSS apply the same end position to all sequences. Can you please check the command line Pise is using and if that is not the cause then send the command line and example inputs. regards, Peter Rice From Marc.Logghe at ablynx.com Wed May 14 11:53:12 2008 From: Marc.Logghe at ablynx.com (Marc Logghe) Date: Wed, 14 May 2008 17:53:12 +0200 Subject: [EMBOSS] transeq feature/bug In-Reply-To: <03C512635899144083CADB0EE222018901AB14E3@alpaca.lan.ablynx.com> References: <03C512635899144083CADB0EE222018901AB14E3@alpaca.lan.ablynx.com> Message-ID: <03C512635899144083CADB0EE222018901AB17B8@alpaca.lan.ablynx.com> > -----Original Message----- > From: emboss-bounces at lists.open-bio.org [mailto:emboss-bounces at lists.open- > bio.org] On Behalf Of Marc Logghe > Sent: Wednesday, May 14, 2008 10:14 AM > To: emboss at emboss.open-bio.org > Subject: [EMBOSS] transeq feature/bug > > Hi all, > > A Pise user reported the following issue when running transeq: the > resulting translation is dependant on the order of the input sequences. > > As it seems, transeq takes the length of the first sequence and uses > that range to translate. Which is fine, but that range is used as well > for all the sequences that are coming after, which is wrong. > > If it happens that your first sequence in the list is smaller than the > ones coming after, then all translations are truncated. > > I think that is a bug. > Update. It is not a bug. The issue was an old transeq.acd file hanging around with ' default: "$(sequence.begin)-$(sequence.end)"' for the regions parameter. Sorry for the fuzz and thanks Peter for looking into this. Regards, Marc From staffa at niehs.nih.gov Wed May 14 16:38:49 2008 From: staffa at niehs.nih.gov (Staffa, Nick (NIH/NIEHS)) Date: Wed, 14 May 2008 16:38:49 -0400 Subject: [EMBOSS] emma In-Reply-To: <03C512635899144083CADB0EE222018901AB17B8@alpaca.lan.ablynx.com> Message-ID: Our emma from Jemboss was returning the input sequences in a fasta file without aligning them. >From command line we discovered that we had no clustalw! SysAdmin obtained clustalw2 and made a symbolic link set to 'clustalw' Running clustalw goes OK and generates this identification: ******** CLUSTAL 2.0.7 Multiple Sequence Alignments ******** Command line emma in conjunction with this program generates this error: rpmbuild.niehs.nih.gov> emma Multiple alignment program - interface to ClustalW program Input (gapped) sequence(s): Lemur_align.fasta output sequence set [lemur.aln]: Dendrogram (tree file) from clustalw output file [lemur.dnd]: CLUSTAL 2.0.7 Multiple Sequence Alignments Error: parameter required for /dnamatrix Error: Failed to open filename '00003189B' Problem writing out EMBOSS alignment fileSegmentation fault rpmbuild.niehs.nih.gov> Y?d think the defaults would be sufficient. Y?d think that Jemboss would do a better job of reporting problems. Nick Staffa Telephone: 919-316-4569 (NIEHS: 6-4569) Scientific Computing Support Group NIEHS Information Technology Support Services Contract (Science Task Monitor: Roy W. Reter (reter at niehs.nih.gov) National Institute of Environmental Health Sciences National Institutes of Health Research Triangle Park, North Carolina From pmr at ebi.ac.uk Thu May 15 03:27:47 2008 From: pmr at ebi.ac.uk (Peter Rice) Date: Thu, 15 May 2008 08:27:47 +0100 Subject: [EMBOSS] emma In-Reply-To: References: Message-ID: <482BE5F3.10001@ebi.ac.uk> Staffa, Nick (NIH/NIEHS) wrote: > ******** CLUSTAL 2.0.7 Multiple Sequence Alignments ******** > > Command line emma in conjunction with this program generates this error: > > CLUSTAL 2.0.7 Multiple Sequence Alignments Error: parameter > required for /dnamatrix Error: Failed to open filename '00003189B' There is a bug in emma, not noticed before because Clustalw 1.x tolerated the command line. In emboss/emma.c the code for option dnamatrix should be: dna_matrix = ajAcdGetListSingle( "dnamatrix"); m2c = ajStrGetCharFirst(dna_matrix); if(m2c=='i') ajStrAssignC(&m2str,"iub"); else if(m2c=='c') ajStrAssignC(&m2str,"clustalw"); else if(m2c=='o') ajStrAssignC(&m2str,"own"); (the characters tested for m2c were from another command line option so the dnamatrix option was not being passed to clustalw). Clustalw 1.8.x ignored the empty /dnamatrix string on the commmand line. > Y'd think the defaults would be sufficient. They are now :-) > Y'd think that Jemboss would do a better job of reporting problems. It is always tricky when the error is reported by another application invoked through EMBOSS. My favourite emma error was a Taverna workflow that failed when executing an emma webservice. Clustalw crashed. The cause turned out to be a user-generated FASTA file with bad end of line characters in the sequence so the sequences became part of the first ID and emma launched clustalw with a set of zero length sequences. We "fixed" it by requiring all EMBOSS sequences to have at least one valid character so we can now issue an EMBOSS error. regards, Peter From staffa at niehs.nih.gov Thu May 15 10:40:36 2008 From: staffa at niehs.nih.gov (Staffa, Nick (NIH/NIEHS)) Date: Thu, 15 May 2008 10:40:36 -0400 Subject: [EMBOSS] emma In-Reply-To: <482BE5F3.10001@ebi.ac.uk> Message-ID: Thanks, but Your comment > They are now :-) is cryptic. Our emma.c (/EMBOSS-5.0.0) has this: dna_matrix = ajAcdGetListSingle( "dnamatrix"); m2c = ajStrGetCharFirst(dna_matrix); if(m2c=='b') ajStrAssignC(&m2str,"iub");else if(m2c=='p') ajStrAssignC(&m2str,"clustalw"); else if(m2c=='g') ajStrAssignC(&m2str,"own"); Should we change the if "m2c==" tests to conform to your i,c,o and recompile? On 5/15/08 3:27 AM, "Peter Rice" wrote: > Staffa, Nick (NIH/NIEHS) wrote: >> ******** CLUSTAL 2.0.7 Multiple Sequence Alignments ******** >> >> Command line emma in conjunction with this program generates this error: >> >> CLUSTAL 2.0.7 Multiple Sequence Alignments Error: parameter >> required for /dnamatrix Error: Failed to open filename '00003189B' > > There is a bug in emma, not noticed before because Clustalw 1.x > tolerated the command line. > > In emboss/emma.c the code for option dnamatrix should be: > > dna_matrix = ajAcdGetListSingle( "dnamatrix"); > m2c = ajStrGetCharFirst(dna_matrix); > > if(m2c=='i') > ajStrAssignC(&m2str,"iub"); > else if(m2c=='c') > ajStrAssignC(&m2str,"clustalw"); > else if(m2c=='o') > ajStrAssignC(&m2str,"own"); > > (the characters tested for m2c were from another command line option so > the dnamatrix option was not being passed to clustalw). > > Clustalw 1.8.x ignored the empty /dnamatrix string on the commmand line. > >> Y'd think the defaults would be sufficient. > > They are now :-) > >> Y'd think that Jemboss would do a better job of reporting problems. > > It is always tricky when the error is reported by another application > invoked through EMBOSS. > > My favourite emma error was a Taverna workflow that failed when > executing an emma webservice. Clustalw crashed. The cause turned out to > be a user-generated FASTA file with bad end of line characters in the > sequence so the sequences became part of the first ID and emma launched > clustalw with a set of zero length sequences. We "fixed" it by requiring > all EMBOSS sequences to have at least one valid character so we can now > issue an EMBOSS error. > > regards, > > Peter From charles-listes-emboss at plessy.org Sun May 18 21:34:48 2008 From: charles-listes-emboss at plessy.org (charles-listes-emboss at plessy.org) Date: Mon, 19 May 2008 10:34:48 +0900 Subject: [EMBOSS] emma: problem with filename : please help In-Reply-To: <4818520C.5090200@ebi.ac.uk> References: <4805F7C2.5090903@ebi.ac.uk> <20080418051637.GA3914@kunpuu.plessy.org> <4818520C.5090200@ebi.ac.uk> Message-ID: <20080519013448.GC18771@kunpuu.plessy.org> Le Wed, Apr 30, 2008 at 12:03:40PM +0100, Peter Rice a ?crit : > In emma.c the wrong characters are tested. > > release 5.0.0: > if(m2c=='b') > ajStrAssignC(&m2str,"iub"); > else if(m2c=='p') > ajStrAssignC(&m2str,"clustalw"); > else if(m2c=='g') > ajStrAssignC(&m2str,"own"); > > corrected: > if(m2c=='i') > ajStrAssignC(&m2str,"iub"); > else if(m2c=='c') > ajStrAssignC(&m2str,"clustalw"); > else if(m2c=='o') > ajStrAssignC(&m2str,"own"); Thanks a lot, I have corrected this in Debian's emboss package through the following patch: http://svn.debian.org/wsvn/debian-med/trunk/packages/emboss/trunk/debian/patches/clustalw2-fix.patch?op=file&rev=0&sc=0 Have a nice day, -- Charles Plessy Debian-Med packaging team Wak?, Saitama, Japan From staffa at niehs.nih.gov Tue May 20 10:18:50 2008 From: staffa at niehs.nih.gov (Staffa, Nick (NIH/NIEHS)) Date: Tue, 20 May 2008 10:18:50 -0400 Subject: [EMBOSS] emma: problem with filename : please help In-Reply-To: <20080519013448.GC18771@kunpuu.plessy.org> Message-ID: What is Debian ? On 5/18/08 9:34 PM, "charles-listes-emboss at plessy.org" wrote: > Le Wed, Apr 30, 2008 at 12:03:40PM +0100, Peter Rice a ?crit : > In emma.c the > wrong characters are tested. > > release 5.0.0: > if(m2c=='b') > > ajStrAssignC(&m2str,"iub"); > else if(m2c=='p') > > ajStrAssignC(&m2str,"clustalw"); > else if(m2c=='g') > > ajStrAssignC(&m2str,"own"); > > corrected: > if(m2c=='i') > > ajStrAssignC(&m2str,"iub"); > else if(m2c=='c') > > ajStrAssignC(&m2str,"clustalw"); > else if(m2c=='o') > > ajStrAssignC(&m2str,"own"); Thanks a lot, I have corrected this in Debian's > emboss package through the following > patch: http://svn.debian.org/wsvn/debian-med/trunk/packages/emboss/trunk/debi > an/patches/clustalw2-fix.patch?op=file&rev=0&sc=0 Have a nice day, -- > Charles Plessy Debian-Med packaging team Wak?, Saitama, > Japan _______________________________________________ EMBOSS mailing > list EMBOSS at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/embo > ss From charles-listes-emboss at plessy.org Tue May 20 10:48:04 2008 From: charles-listes-emboss at plessy.org (Charles Plessy) Date: Tue, 20 May 2008 23:48:04 +0900 Subject: [EMBOSS] emma: problem with filename : please help In-Reply-To: References: <20080519013448.GC18771@kunpuu.plessy.org> Message-ID: <20080520144804.GA30428@kunpuu.plessy.org> Le Tue, May 20, 2008 at 10:18:50AM -0400, Staffa, Nick (NIH/NIEHS) a ?crit : > What is Debian ? Vast question :) Debian is an operating system with a strong emphais on software freedom. Phylogenetically, it stems with Unix and its derivatives. It can be run on many hardware platforms, among which most Intel and AMD-based "PC" machines, as well as on Apple computers. It includes powerful command line and graphical user interfaces, on both of which EMBOSS can be used. The Debian-Med project aims at bringing free software for medecine an biology to Debian users, and distributes pre-compiled packages that allow to run EMBOSS immediately after download. You can find more information on the following pages: http://www.debian.org http://www.debian.org/devel/debian-med http://packages.debian.org/sid/emboss (I realise that I wrote the above paragraph in a very "for a broad audience" style. Please do not feel offended if the only answer you needed was just "Debian is a Linux distrubution"! ) Have a nice day, -- Charles Plessy, Debian-Med packaging team From scott at cs.wits.ac.za Wed May 21 07:15:00 2008 From: scott at cs.wits.ac.za (Scott Hazelhurst) Date: Wed, 21 May 2008 13:15:00 +0200 Subject: [EMBOSS] EMBOSS wrappers for wcd EST clustering program Message-ID: A new version of the wcd tool for clustering expressed sequence tags and the EMBOSS wrappers for wcd are available from http://code.google.com/p/wcdest Scott

This communication is intended for the addressee only. It is confidential. If you have received this communication in error, please notify us immediately and destroy the original message. You may not copy or disseminate this communication without the permission of the University. Only authorized signatories are competent to enter into agreements on behalf of the University and recipients are thus advised that the content of this message may not be legally binding on the University and may contain the personal views and opinions of the author, which are not necessarily the views and opinions of The University of the Witwatersrand, Johannesburg. All agreements between the University and outsiders are subject to South African Law unless the University agrees in writing to the contrary.

From Ronald.C.Mackenzie at uth.tmc.edu Thu May 22 11:11:45 2008 From: Ronald.C.Mackenzie at uth.tmc.edu (Mackenzie, Ronald C) Date: Thu, 22 May 2008 10:11:45 -0500 Subject: [EMBOSS] Jemboss setup problem Message-ID: I have trying to set up Jemboss on Solaris 10 (SPARC) and everything seems to compile okay and exit gracefully at the .configure, make, make install stages. I put the appropriate lines for setenv in the .cshrc and now when I follow the last few lines (section 3.) in the Jemboss installation notes http://emboss.sourceforge.net/Jemboss/install/standalone.html )I get the following: bearcat# java org/emboss/jemboss/Jemboss local & [1] 28597 bearcat# Java Accessibility Bridge for GNOME loaded. Exit value:: 9 Exit value:: 9 If I now hit enter and type in: bearcat# ./runJemboss.sh bearcat# Exit value:: 9 Exit value:: 9 If I look at the running processes: bearcat# ps PID TTY TIME CMD 28602 pts/5 0:16 java 28605 pts/5 0:00 ps 28559 pts/5 0:00 sh 28581 pts/5 0:00 csh 28597 pts/5 1:10 java But nothing else happens. It just sits there and a java window never appears. Anyone got any ideas? Or do you know what an "Exit value:: 9" means. I couldn't find anything like when I searched the archives. Thanks in advance for your help, Chris From uludag at ebi.ac.uk Thu May 22 12:23:05 2008 From: uludag at ebi.ac.uk (Mahmut Uludag) Date: Thu, 22 May 2008 17:23:05 +0100 Subject: [EMBOSS] Jemboss setup problem In-Reply-To: References: Message-ID: <1211473385.30918.105.camel@emboss2.ebi.ac.uk> > bearcat# java org/emboss/jemboss/Jemboss local & You shouldn't normally start Jemboss directly but use the runJemboss.sh script (it sets the Java classpath and the environment). Make sure that you have edited your runJemboss.sh script and added the word 'local' in the line java is invoked, you should have something similar to the following. /myjre/bin/java org.emboss.jemboss.Jemboss & Which version of Java are you using? I ask this because when I do the same mistake I get different error messages. Regards, Mahmut From uludag at ebi.ac.uk Thu May 22 14:45:08 2008 From: uludag at ebi.ac.uk (uludag at ebi.ac.uk) Date: Thu, 22 May 2008 19:45:08 +0100 (BST) Subject: [EMBOSS] Jemboss setup problem In-Reply-To: References: <1211473385.30918.105.camel@emboss2.ebi.ac.uk> Message-ID: <58412.86.141.181.27.1211481908.squirrel@webmail.ebi.ac.uk> > But I am not quite there yet. I have two other "problems" and one other > question. Part of my problem is my lack of familiarity with the GUI > interface. I have been using EMBOSS on the command line for quite some > time. Anyway with Jemboss when I run the runJemboss.sh script a little > box pops up asking for a username and password (it looks like a login > for a remote server). Do you have any idea what that is for? Do I have > to comment out something in the runJemboss.sh script to stop it running? You might have "user.auth=true" in your jemboss.properties file which might be found in your share/EMBOSS/jemboss/resources/ directory under your jemboss installation folder or it might be in your home directory. Setting this property to false may help. > The other problem I am having is that when I use pepstats on the command > line on the file at this link: > https://webspace.uth.tmc.edu/rmackenzie/public/orf_trans_all_assembly_21 > .fasta > I get a result in about 2 seconds. But when I try doing this through > Jemboss it just sits there with the hourglass going. > I have also tried this using the windows XP version of Jemboss, running > on my dual core 2 Gb of RAM PC at my house. I ran it for 12 hours and > still go no output. If you have a Jemboss running there could you try > running the file through pepstats for me? I think it is a bug and if so > I should report it. By the way I tried stripping out the * for the stop > codons but it made no difference. I'm able to reproduce this problem and will return you tomorrow with more details. I initially thought giving more memory to Java may help to solve the problem but it doesn't. > And the final question. Do other users of this list normally post > replies to the list? I think it depends on the post. It is good to post to the list when you think others may also hit the same problem. Regards, Mahmut From staffa at niehs.nih.gov Wed May 28 14:22:28 2008 From: staffa at niehs.nih.gov (Staffa, Nick (NIH/NIEHS)) Date: Wed, 28 May 2008 14:22:28 -0400 Subject: [EMBOSS] Dot Plot Message-ID: I am doing a genomic survey of sorts. I generate a lot of X,Y coordinates. I would like to make a plot of these. Emboss Dot Plot programs all take sequence as input. What do you suggest? From gbottu at vub.ac.be Thu May 29 05:53:52 2008 From: gbottu at vub.ac.be (Guy Bottu) Date: Thu, 29 May 2008 11:53:52 +0200 Subject: [EMBOSS] Dot Plot In-Reply-To: References: Message-ID: <483E7D30.4050904@vub.ac.be> Staffa, Nick (NIH/NIEHS) wrote: > I am doing a genomic survey of sorts. > I generate a lot of X,Y coordinates. > I would like to make a plot of these. If you have still a copy of GCG lingering around : GCG has separate programs to compute the XY-coordinates and actually draw the plot (dotplot). You will of course need to write a Perl script to put the coordinates in the format used by dotplot. Another possibility I can think about are tools created by the UCSC. If you can get your coordinates in the right lav-like format (tricky, because it are not individual dots but rather stright line segments), you could use the LAJ Java application (interactive) or the mkdotplot program from the PipMaker server (creates PostScript file). You can look at http://oryx.ulb.ac.be/embosshelp/blastz.html#output to get a snapshot how the input ada.blastz and the output ada.blastz.dotplot.pdf look like. Regards, Guy Bottu, Belgian EMBnet Node From staffa at niehs.nih.gov Thu May 29 08:21:30 2008 From: staffa at niehs.nih.gov (Staffa, Nick (NIH/NIEHS)) Date: Thu, 29 May 2008 08:21:30 -0400 Subject: [EMBOSS] Dot Plot In-Reply-To: <483E7D30.4050904@vub.ac.be> Message-ID: Thanks. After a day of futzing around trying to create the point file that GCG's Compare makes, with an whole page of Perl, I attacked the figure file it makes. If one doesnt care about axes, then 2 or 3 commands set up the window and one adds his points in the original units ? a half page of perl. Figure is a great program. It's so old that surely they could open source it. On 5/29/08 5:53 AM, "Guy Bottu" wrote: > Staffa, Nick (NIH/NIEHS) wrote: >> I am doing a genomic survey of sorts. >> I generate a lot of X,Y coordinates. >> I would like to make a plot of these. > > If you have still a copy of GCG lingering around : GCG has separate programs > to > compute the XY-coordinates and actually draw the plot (dotplot). You will of > course need to write a Perl script to put the coordinates in the format used > by > dotplot. > > Another possibility I can think about are tools created by the UCSC. If you > can > get your coordinates in the right lav-like format (tricky, because it are not > individual dots but rather stright line segments), you could use the LAJ Java > application (interactive) or the mkdotplot program from the PipMaker server > (creates PostScript file). You can look at > http://oryx.ulb.ac.be/embosshelp/blastz.html#output > to get a snapshot how the input ada.blastz and the output > ada.blastz.dotplot.pdf > look like. > > Regards, > Guy Bottu, > Belgian EMBnet Node > > > From gbottu at vub.ac.be Fri May 30 04:55:15 2008 From: gbottu at vub.ac.be (Guy Bottu) Date: Fri, 30 May 2008 10:55:15 +0200 Subject: [EMBOSS] Dot Plot In-Reply-To: References: Message-ID: <483FC0F3.8050309@vub.ac.be> Staffa, Nick (NIH/NIEHS) wrote: > After a day of futzing around trying to create the point file that GCG's > Compare makes, with an whole page of Perl, I attacked the figure file it > makes. If one doesnt care about axes, then 2 or 3 commands set up the window > and one adds his points in the original units ? a half page of perl. > Figure is a great program. It's so old that surely they could open source > it. That has been discussed a lot these days. Since they have abandonned the idea of making cash from it, why could they not make the very useful SeqLab or even all their software OpenSource ? But anyway, there is the GCGfigure program that runs on old MacOS and has always been freeware. Guy From A.J.Pemberton at bham.ac.uk Fri May 30 05:27:41 2008 From: A.J.Pemberton at bham.ac.uk (Anthony Pemberton) Date: Fri, 30 May 2008 10:27:41 +0100 Subject: [EMBOSS] Dot Plot In-Reply-To: <483FC0F3.8050309@vub.ac.be> References: <483FC0F3.8050309@vub.ac.be> Message-ID: Nick, If you have simple X,Y coordinate data, could I suggest Grace? http://plasma-gate.weizmann.ac.il/Grace/ Regards, Tony P. > -----Original Message----- > From: emboss-bounces at lists.open-bio.org [mailto:emboss- > bounces at lists.open-bio.org] On Behalf Of Guy Bottu > Sent: 30 May 2008 09:55 > To: Staffa, Nick (NIH/NIEHS) > Cc: Rodgers, Gary (NIH/NIEHS) [C]; Young,Reeves (NIH/NIEHS) [C]; > emboss at lists.open-bio.org > Subject: Re: [EMBOSS] Dot Plot > > Staffa, Nick (NIH/NIEHS) wrote: > > After a day of futzing around trying to create the point file that > GCG's > > Compare makes, with an whole page of Perl, I attacked the figure file > it > > makes. If one doesnt care about axes, then 2 or 3 commands set up the > window > > and one adds his points in the original units - a half page of perl. > > Figure is a great program. It's so old that surely they could open > source > > it. > > That has been discussed a lot these days. Since they have abandonned > the idea of > making cash from it, why could they not make the very useful SeqLab or > even all > their software OpenSource ? But anyway, there is the GCGfigure program > that runs > on old MacOS and has always been freeware. > > Guy > > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss From uludag at ebi.ac.uk Thu May 1 16:23:09 2008 From: uludag at ebi.ac.uk (Mahmut Uludag) Date: Thu, 01 May 2008 17:23:09 +0100 Subject: [EMBOSS] Help/Info in Jemboss In-Reply-To: References: Message-ID: <1209658990.14653.90.camel@emboss2.ebi.ac.uk> > When on goes to run an EMBOSS program from Jemboss, there is a little dark > blue icon with an ?i? in it. Clicking on this produces this message: > > A real web site is > http://emboss.sourceforge.net/apps/release/4.0/emboss/apps/seqret.html > BUT the URL in the window has a tandem duplication of ?apps/? > > How can this be ameliorated? > > The part up thru the first apps is embossURL in jemboss.resources. > Should this be truncated? Yes. The URL should also point to release 5.0. I will fix the extra "apps" bit and will find a way to avoid URLs with wrong version numbers in future releases. Regards, Mahmut From ajb at ebi.ac.uk Mon May 5 16:33:48 2008 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Mon, 5 May 2008 17:33:48 +0100 (BST) Subject: [EMBOSS] [Fwd: BOSC 2008 Announcement and Call For Submissions] Message-ID: <34936.86.14.232.77.1210005228.squirrel@webmail.ebi.ac.uk> ---------------------------- Original Message ---------------------------- Subject: BOSC 2008 Announcement and Call For Submissions From: darin.london at duke.edu Date: Mon, May 5, 2008 3:08 pm To: emboss-owner at lists.open-bio.org -------------------------------------------------------------------------- BOSC 2008 Call for Abstracts Reminder The 9th annual Bioinformatics Open Source Conference (BOSC 2008) will take place in Toronto, Ontario, Canada, as one of several Special Interest Group (SIG) meetings occurring in conjunction with the 16th annual Intelligent Systems for Molecular Biology Conference (ISMB 2008). This is the final reminder to submit your proposals for talks to the BOSC submission system before May 11. Submission Process: All abstracts must be submitted through our Open Conference Systems site (http://events.open-bio.org/BOSC2008/openconf.php). The form will ask for a small Abstract Text to be pasted into it, and a full paper. The small Abstract text should be a summary, while the longer abstract (should provide more details, including the open-source license requirement details) Full-length abstracts are limited to one page with one inch (2.5 cm) margins on the top, sides, and bottom. The full-length abstract should include the title, authors, and affiliations. We prefer your abstract to be in PDF format, although plain t Important Dates: May 11: Abstract submission deadline. June 2: Notification of accepted talks. June 4: Early registration discount cut-off. July 18-19: BOSC 2008! We hope to see you at BOSC 2008! Kam Dahlquist and Darin London BOSC 2008 Co-organizers From Marc.Logghe at ablynx.com Wed May 14 08:14:29 2008 From: Marc.Logghe at ablynx.com (Marc Logghe) Date: Wed, 14 May 2008 10:14:29 +0200 Subject: [EMBOSS] transeq feature/bug Message-ID: <03C512635899144083CADB0EE222018901AB14E3@alpaca.lan.ablynx.com> Hi all, A Pise user reported the following issue when running transeq: the resulting translation is dependant on the order of the input sequences. As it seems, transeq takes the length of the first sequence and uses that range to translate. Which is fine, but that range is used as well for all the sequences that are coming after, which is wrong. If it happens that your first sequence in the list is smaller than the ones coming after, then all translations are truncated. I think that is a bug. Embossversion 5.0.0. Regards, Marc From pmr at ebi.ac.uk Wed May 14 09:53:38 2008 From: pmr at ebi.ac.uk (Peter Rice) Date: Wed, 14 May 2008 10:53:38 +0100 Subject: [EMBOSS] transeq feature/bug In-Reply-To: <03C512635899144083CADB0EE222018901AB14E3@alpaca.lan.ablynx.com> References: <03C512635899144083CADB0EE222018901AB14E3@alpaca.lan.ablynx.com> Message-ID: <482AB6A2.3070807@ebi.ac.uk> Marc Logghe wrote: > Hi all, > > A Pise user reported the following issue when running transeq: the > resulting translation is dependant on the order of the input sequences. > > As it seems, transeq takes the length of the first sequence and uses > that range to translate. Which is fine, but that range is used as well > for all the sequences that are coming after, which is wrong. > > If it happens that your first sequence in the list is smaller than the > ones coming after, then all translations are truncated. > > I think that is a bug. Strange - we have QA tests for exactly those cases and they are working in releases 5.0.0 and earlier releases. Ah, but perhaps this is a Pise problem. If Pise is putting -send on the command line with the length of the first sequence, then this will make EMBOSS apply the same end position to all sequences. Can you please check the command line Pise is using and if that is not the cause then send the command line and example inputs. regards, Peter Rice From Marc.Logghe at ablynx.com Wed May 14 15:53:12 2008 From: Marc.Logghe at ablynx.com (Marc Logghe) Date: Wed, 14 May 2008 17:53:12 +0200 Subject: [EMBOSS] transeq feature/bug In-Reply-To: <03C512635899144083CADB0EE222018901AB14E3@alpaca.lan.ablynx.com> References: <03C512635899144083CADB0EE222018901AB14E3@alpaca.lan.ablynx.com> Message-ID: <03C512635899144083CADB0EE222018901AB17B8@alpaca.lan.ablynx.com> > -----Original Message----- > From: emboss-bounces at lists.open-bio.org [mailto:emboss-bounces at lists.open- > bio.org] On Behalf Of Marc Logghe > Sent: Wednesday, May 14, 2008 10:14 AM > To: emboss at emboss.open-bio.org > Subject: [EMBOSS] transeq feature/bug > > Hi all, > > A Pise user reported the following issue when running transeq: the > resulting translation is dependant on the order of the input sequences. > > As it seems, transeq takes the length of the first sequence and uses > that range to translate. Which is fine, but that range is used as well > for all the sequences that are coming after, which is wrong. > > If it happens that your first sequence in the list is smaller than the > ones coming after, then all translations are truncated. > > I think that is a bug. > Update. It is not a bug. The issue was an old transeq.acd file hanging around with ' default: "$(sequence.begin)-$(sequence.end)"' for the regions parameter. Sorry for the fuzz and thanks Peter for looking into this. Regards, Marc From staffa at niehs.nih.gov Wed May 14 20:38:49 2008 From: staffa at niehs.nih.gov (Staffa, Nick (NIH/NIEHS)) Date: Wed, 14 May 2008 16:38:49 -0400 Subject: [EMBOSS] emma In-Reply-To: <03C512635899144083CADB0EE222018901AB17B8@alpaca.lan.ablynx.com> Message-ID: Our emma from Jemboss was returning the input sequences in a fasta file without aligning them. >From command line we discovered that we had no clustalw! SysAdmin obtained clustalw2 and made a symbolic link set to 'clustalw' Running clustalw goes OK and generates this identification: ******** CLUSTAL 2.0.7 Multiple Sequence Alignments ******** Command line emma in conjunction with this program generates this error: rpmbuild.niehs.nih.gov> emma Multiple alignment program - interface to ClustalW program Input (gapped) sequence(s): Lemur_align.fasta output sequence set [lemur.aln]: Dendrogram (tree file) from clustalw output file [lemur.dnd]: CLUSTAL 2.0.7 Multiple Sequence Alignments Error: parameter required for /dnamatrix Error: Failed to open filename '00003189B' Problem writing out EMBOSS alignment fileSegmentation fault rpmbuild.niehs.nih.gov> Y?d think the defaults would be sufficient. Y?d think that Jemboss would do a better job of reporting problems. Nick Staffa Telephone: 919-316-4569 (NIEHS: 6-4569) Scientific Computing Support Group NIEHS Information Technology Support Services Contract (Science Task Monitor: Roy W. Reter (reter at niehs.nih.gov) National Institute of Environmental Health Sciences National Institutes of Health Research Triangle Park, North Carolina From pmr at ebi.ac.uk Thu May 15 07:27:47 2008 From: pmr at ebi.ac.uk (Peter Rice) Date: Thu, 15 May 2008 08:27:47 +0100 Subject: [EMBOSS] emma In-Reply-To: References: Message-ID: <482BE5F3.10001@ebi.ac.uk> Staffa, Nick (NIH/NIEHS) wrote: > ******** CLUSTAL 2.0.7 Multiple Sequence Alignments ******** > > Command line emma in conjunction with this program generates this error: > > CLUSTAL 2.0.7 Multiple Sequence Alignments Error: parameter > required for /dnamatrix Error: Failed to open filename '00003189B' There is a bug in emma, not noticed before because Clustalw 1.x tolerated the command line. In emboss/emma.c the code for option dnamatrix should be: dna_matrix = ajAcdGetListSingle( "dnamatrix"); m2c = ajStrGetCharFirst(dna_matrix); if(m2c=='i') ajStrAssignC(&m2str,"iub"); else if(m2c=='c') ajStrAssignC(&m2str,"clustalw"); else if(m2c=='o') ajStrAssignC(&m2str,"own"); (the characters tested for m2c were from another command line option so the dnamatrix option was not being passed to clustalw). Clustalw 1.8.x ignored the empty /dnamatrix string on the commmand line. > Y'd think the defaults would be sufficient. They are now :-) > Y'd think that Jemboss would do a better job of reporting problems. It is always tricky when the error is reported by another application invoked through EMBOSS. My favourite emma error was a Taverna workflow that failed when executing an emma webservice. Clustalw crashed. The cause turned out to be a user-generated FASTA file with bad end of line characters in the sequence so the sequences became part of the first ID and emma launched clustalw with a set of zero length sequences. We "fixed" it by requiring all EMBOSS sequences to have at least one valid character so we can now issue an EMBOSS error. regards, Peter From staffa at niehs.nih.gov Thu May 15 14:40:36 2008 From: staffa at niehs.nih.gov (Staffa, Nick (NIH/NIEHS)) Date: Thu, 15 May 2008 10:40:36 -0400 Subject: [EMBOSS] emma In-Reply-To: <482BE5F3.10001@ebi.ac.uk> Message-ID: Thanks, but Your comment > They are now :-) is cryptic. Our emma.c (/EMBOSS-5.0.0) has this: dna_matrix = ajAcdGetListSingle( "dnamatrix"); m2c = ajStrGetCharFirst(dna_matrix); if(m2c=='b') ajStrAssignC(&m2str,"iub");else if(m2c=='p') ajStrAssignC(&m2str,"clustalw"); else if(m2c=='g') ajStrAssignC(&m2str,"own"); Should we change the if "m2c==" tests to conform to your i,c,o and recompile? On 5/15/08 3:27 AM, "Peter Rice" wrote: > Staffa, Nick (NIH/NIEHS) wrote: >> ******** CLUSTAL 2.0.7 Multiple Sequence Alignments ******** >> >> Command line emma in conjunction with this program generates this error: >> >> CLUSTAL 2.0.7 Multiple Sequence Alignments Error: parameter >> required for /dnamatrix Error: Failed to open filename '00003189B' > > There is a bug in emma, not noticed before because Clustalw 1.x > tolerated the command line. > > In emboss/emma.c the code for option dnamatrix should be: > > dna_matrix = ajAcdGetListSingle( "dnamatrix"); > m2c = ajStrGetCharFirst(dna_matrix); > > if(m2c=='i') > ajStrAssignC(&m2str,"iub"); > else if(m2c=='c') > ajStrAssignC(&m2str,"clustalw"); > else if(m2c=='o') > ajStrAssignC(&m2str,"own"); > > (the characters tested for m2c were from another command line option so > the dnamatrix option was not being passed to clustalw). > > Clustalw 1.8.x ignored the empty /dnamatrix string on the commmand line. > >> Y'd think the defaults would be sufficient. > > They are now :-) > >> Y'd think that Jemboss would do a better job of reporting problems. > > It is always tricky when the error is reported by another application > invoked through EMBOSS. > > My favourite emma error was a Taverna workflow that failed when > executing an emma webservice. Clustalw crashed. The cause turned out to > be a user-generated FASTA file with bad end of line characters in the > sequence so the sequences became part of the first ID and emma launched > clustalw with a set of zero length sequences. We "fixed" it by requiring > all EMBOSS sequences to have at least one valid character so we can now > issue an EMBOSS error. > > regards, > > Peter From charles-listes-emboss at plessy.org Mon May 19 01:34:48 2008 From: charles-listes-emboss at plessy.org (charles-listes-emboss at plessy.org) Date: Mon, 19 May 2008 10:34:48 +0900 Subject: [EMBOSS] emma: problem with filename : please help In-Reply-To: <4818520C.5090200@ebi.ac.uk> References: <4805F7C2.5090903@ebi.ac.uk> <20080418051637.GA3914@kunpuu.plessy.org> <4818520C.5090200@ebi.ac.uk> Message-ID: <20080519013448.GC18771@kunpuu.plessy.org> Le Wed, Apr 30, 2008 at 12:03:40PM +0100, Peter Rice a ?crit : > In emma.c the wrong characters are tested. > > release 5.0.0: > if(m2c=='b') > ajStrAssignC(&m2str,"iub"); > else if(m2c=='p') > ajStrAssignC(&m2str,"clustalw"); > else if(m2c=='g') > ajStrAssignC(&m2str,"own"); > > corrected: > if(m2c=='i') > ajStrAssignC(&m2str,"iub"); > else if(m2c=='c') > ajStrAssignC(&m2str,"clustalw"); > else if(m2c=='o') > ajStrAssignC(&m2str,"own"); Thanks a lot, I have corrected this in Debian's emboss package through the following patch: http://svn.debian.org/wsvn/debian-med/trunk/packages/emboss/trunk/debian/patches/clustalw2-fix.patch?op=file&rev=0&sc=0 Have a nice day, -- Charles Plessy Debian-Med packaging team Wak?, Saitama, Japan From staffa at niehs.nih.gov Tue May 20 14:18:50 2008 From: staffa at niehs.nih.gov (Staffa, Nick (NIH/NIEHS)) Date: Tue, 20 May 2008 10:18:50 -0400 Subject: [EMBOSS] emma: problem with filename : please help In-Reply-To: <20080519013448.GC18771@kunpuu.plessy.org> Message-ID: What is Debian ? On 5/18/08 9:34 PM, "charles-listes-emboss at plessy.org" wrote: > Le Wed, Apr 30, 2008 at 12:03:40PM +0100, Peter Rice a ?crit : > In emma.c the > wrong characters are tested. > > release 5.0.0: > if(m2c=='b') > > ajStrAssignC(&m2str,"iub"); > else if(m2c=='p') > > ajStrAssignC(&m2str,"clustalw"); > else if(m2c=='g') > > ajStrAssignC(&m2str,"own"); > > corrected: > if(m2c=='i') > > ajStrAssignC(&m2str,"iub"); > else if(m2c=='c') > > ajStrAssignC(&m2str,"clustalw"); > else if(m2c=='o') > > ajStrAssignC(&m2str,"own"); Thanks a lot, I have corrected this in Debian's > emboss package through the following > patch: http://svn.debian.org/wsvn/debian-med/trunk/packages/emboss/trunk/debi > an/patches/clustalw2-fix.patch?op=file&rev=0&sc=0 Have a nice day, -- > Charles Plessy Debian-Med packaging team Wak?, Saitama, > Japan _______________________________________________ EMBOSS mailing > list EMBOSS at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/embo > ss From charles-listes-emboss at plessy.org Tue May 20 14:48:04 2008 From: charles-listes-emboss at plessy.org (Charles Plessy) Date: Tue, 20 May 2008 23:48:04 +0900 Subject: [EMBOSS] emma: problem with filename : please help In-Reply-To: References: <20080519013448.GC18771@kunpuu.plessy.org> Message-ID: <20080520144804.GA30428@kunpuu.plessy.org> Le Tue, May 20, 2008 at 10:18:50AM -0400, Staffa, Nick (NIH/NIEHS) a ?crit : > What is Debian ? Vast question :) Debian is an operating system with a strong emphais on software freedom. Phylogenetically, it stems with Unix and its derivatives. It can be run on many hardware platforms, among which most Intel and AMD-based "PC" machines, as well as on Apple computers. It includes powerful command line and graphical user interfaces, on both of which EMBOSS can be used. The Debian-Med project aims at bringing free software for medecine an biology to Debian users, and distributes pre-compiled packages that allow to run EMBOSS immediately after download. You can find more information on the following pages: http://www.debian.org http://www.debian.org/devel/debian-med http://packages.debian.org/sid/emboss (I realise that I wrote the above paragraph in a very "for a broad audience" style. Please do not feel offended if the only answer you needed was just "Debian is a Linux distrubution"! ) Have a nice day, -- Charles Plessy, Debian-Med packaging team From scott at cs.wits.ac.za Wed May 21 11:15:00 2008 From: scott at cs.wits.ac.za (Scott Hazelhurst) Date: Wed, 21 May 2008 13:15:00 +0200 Subject: [EMBOSS] EMBOSS wrappers for wcd EST clustering program Message-ID: A new version of the wcd tool for clustering expressed sequence tags and the EMBOSS wrappers for wcd are available from http://code.google.com/p/wcdest Scott

This communication is intended for the addressee only. It is confidential. If you have received this communication in error, please notify us immediately and destroy the original message. You may not copy or disseminate this communication without the permission of the University. Only authorized signatories are competent to enter into agreements on behalf of the University and recipients are thus advised that the content of this message may not be legally binding on the University and may contain the personal views and opinions of the author, which are not necessarily the views and opinions of The University of the Witwatersrand, Johannesburg. All agreements between the University and outsiders are subject to South African Law unless the University agrees in writing to the contrary.

From Ronald.C.Mackenzie at uth.tmc.edu Thu May 22 15:11:45 2008 From: Ronald.C.Mackenzie at uth.tmc.edu (Mackenzie, Ronald C) Date: Thu, 22 May 2008 10:11:45 -0500 Subject: [EMBOSS] Jemboss setup problem Message-ID: I have trying to set up Jemboss on Solaris 10 (SPARC) and everything seems to compile okay and exit gracefully at the .configure, make, make install stages. I put the appropriate lines for setenv in the .cshrc and now when I follow the last few lines (section 3.) in the Jemboss installation notes http://emboss.sourceforge.net/Jemboss/install/standalone.html )I get the following: bearcat# java org/emboss/jemboss/Jemboss local & [1] 28597 bearcat# Java Accessibility Bridge for GNOME loaded. Exit value:: 9 Exit value:: 9 If I now hit enter and type in: bearcat# ./runJemboss.sh bearcat# Exit value:: 9 Exit value:: 9 If I look at the running processes: bearcat# ps PID TTY TIME CMD 28602 pts/5 0:16 java 28605 pts/5 0:00 ps 28559 pts/5 0:00 sh 28581 pts/5 0:00 csh 28597 pts/5 1:10 java But nothing else happens. It just sits there and a java window never appears. Anyone got any ideas? Or do you know what an "Exit value:: 9" means. I couldn't find anything like when I searched the archives. Thanks in advance for your help, Chris From uludag at ebi.ac.uk Thu May 22 16:23:05 2008 From: uludag at ebi.ac.uk (Mahmut Uludag) Date: Thu, 22 May 2008 17:23:05 +0100 Subject: [EMBOSS] Jemboss setup problem In-Reply-To: References: Message-ID: <1211473385.30918.105.camel@emboss2.ebi.ac.uk> > bearcat# java org/emboss/jemboss/Jemboss local & You shouldn't normally start Jemboss directly but use the runJemboss.sh script (it sets the Java classpath and the environment). Make sure that you have edited your runJemboss.sh script and added the word 'local' in the line java is invoked, you should have something similar to the following. /myjre/bin/java org.emboss.jemboss.Jemboss & Which version of Java are you using? I ask this because when I do the same mistake I get different error messages. Regards, Mahmut From uludag at ebi.ac.uk Thu May 22 18:45:08 2008 From: uludag at ebi.ac.uk (uludag at ebi.ac.uk) Date: Thu, 22 May 2008 19:45:08 +0100 (BST) Subject: [EMBOSS] Jemboss setup problem In-Reply-To: References: <1211473385.30918.105.camel@emboss2.ebi.ac.uk> Message-ID: <58412.86.141.181.27.1211481908.squirrel@webmail.ebi.ac.uk> > But I am not quite there yet. I have two other "problems" and one other > question. Part of my problem is my lack of familiarity with the GUI > interface. I have been using EMBOSS on the command line for quite some > time. Anyway with Jemboss when I run the runJemboss.sh script a little > box pops up asking for a username and password (it looks like a login > for a remote server). Do you have any idea what that is for? Do I have > to comment out something in the runJemboss.sh script to stop it running? You might have "user.auth=true" in your jemboss.properties file which might be found in your share/EMBOSS/jemboss/resources/ directory under your jemboss installation folder or it might be in your home directory. Setting this property to false may help. > The other problem I am having is that when I use pepstats on the command > line on the file at this link: > https://webspace.uth.tmc.edu/rmackenzie/public/orf_trans_all_assembly_21 > .fasta > I get a result in about 2 seconds. But when I try doing this through > Jemboss it just sits there with the hourglass going. > I have also tried this using the windows XP version of Jemboss, running > on my dual core 2 Gb of RAM PC at my house. I ran it for 12 hours and > still go no output. If you have a Jemboss running there could you try > running the file through pepstats for me? I think it is a bug and if so > I should report it. By the way I tried stripping out the * for the stop > codons but it made no difference. I'm able to reproduce this problem and will return you tomorrow with more details. I initially thought giving more memory to Java may help to solve the problem but it doesn't. > And the final question. Do other users of this list normally post > replies to the list? I think it depends on the post. It is good to post to the list when you think others may also hit the same problem. Regards, Mahmut From staffa at niehs.nih.gov Wed May 28 18:22:28 2008 From: staffa at niehs.nih.gov (Staffa, Nick (NIH/NIEHS)) Date: Wed, 28 May 2008 14:22:28 -0400 Subject: [EMBOSS] Dot Plot Message-ID: I am doing a genomic survey of sorts. I generate a lot of X,Y coordinates. I would like to make a plot of these. Emboss Dot Plot programs all take sequence as input. What do you suggest? From gbottu at vub.ac.be Thu May 29 09:53:52 2008 From: gbottu at vub.ac.be (Guy Bottu) Date: Thu, 29 May 2008 11:53:52 +0200 Subject: [EMBOSS] Dot Plot In-Reply-To: References: Message-ID: <483E7D30.4050904@vub.ac.be> Staffa, Nick (NIH/NIEHS) wrote: > I am doing a genomic survey of sorts. > I generate a lot of X,Y coordinates. > I would like to make a plot of these. If you have still a copy of GCG lingering around : GCG has separate programs to compute the XY-coordinates and actually draw the plot (dotplot). You will of course need to write a Perl script to put the coordinates in the format used by dotplot. Another possibility I can think about are tools created by the UCSC. If you can get your coordinates in the right lav-like format (tricky, because it are not individual dots but rather stright line segments), you could use the LAJ Java application (interactive) or the mkdotplot program from the PipMaker server (creates PostScript file). You can look at http://oryx.ulb.ac.be/embosshelp/blastz.html#output to get a snapshot how the input ada.blastz and the output ada.blastz.dotplot.pdf look like. Regards, Guy Bottu, Belgian EMBnet Node From staffa at niehs.nih.gov Thu May 29 12:21:30 2008 From: staffa at niehs.nih.gov (Staffa, Nick (NIH/NIEHS)) Date: Thu, 29 May 2008 08:21:30 -0400 Subject: [EMBOSS] Dot Plot In-Reply-To: <483E7D30.4050904@vub.ac.be> Message-ID: Thanks. After a day of futzing around trying to create the point file that GCG's Compare makes, with an whole page of Perl, I attacked the figure file it makes. If one doesnt care about axes, then 2 or 3 commands set up the window and one adds his points in the original units ? a half page of perl. Figure is a great program. It's so old that surely they could open source it. On 5/29/08 5:53 AM, "Guy Bottu" wrote: > Staffa, Nick (NIH/NIEHS) wrote: >> I am doing a genomic survey of sorts. >> I generate a lot of X,Y coordinates. >> I would like to make a plot of these. > > If you have still a copy of GCG lingering around : GCG has separate programs > to > compute the XY-coordinates and actually draw the plot (dotplot). You will of > course need to write a Perl script to put the coordinates in the format used > by > dotplot. > > Another possibility I can think about are tools created by the UCSC. If you > can > get your coordinates in the right lav-like format (tricky, because it are not > individual dots but rather stright line segments), you could use the LAJ Java > application (interactive) or the mkdotplot program from the PipMaker server > (creates PostScript file). You can look at > http://oryx.ulb.ac.be/embosshelp/blastz.html#output > to get a snapshot how the input ada.blastz and the output > ada.blastz.dotplot.pdf > look like. > > Regards, > Guy Bottu, > Belgian EMBnet Node > > > From gbottu at vub.ac.be Fri May 30 08:55:15 2008 From: gbottu at vub.ac.be (Guy Bottu) Date: Fri, 30 May 2008 10:55:15 +0200 Subject: [EMBOSS] Dot Plot In-Reply-To: References: Message-ID: <483FC0F3.8050309@vub.ac.be> Staffa, Nick (NIH/NIEHS) wrote: > After a day of futzing around trying to create the point file that GCG's > Compare makes, with an whole page of Perl, I attacked the figure file it > makes. If one doesnt care about axes, then 2 or 3 commands set up the window > and one adds his points in the original units ? a half page of perl. > Figure is a great program. It's so old that surely they could open source > it. That has been discussed a lot these days. Since they have abandonned the idea of making cash from it, why could they not make the very useful SeqLab or even all their software OpenSource ? But anyway, there is the GCGfigure program that runs on old MacOS and has always been freeware. Guy From A.J.Pemberton at bham.ac.uk Fri May 30 09:27:41 2008 From: A.J.Pemberton at bham.ac.uk (Anthony Pemberton) Date: Fri, 30 May 2008 10:27:41 +0100 Subject: [EMBOSS] Dot Plot In-Reply-To: <483FC0F3.8050309@vub.ac.be> References: <483FC0F3.8050309@vub.ac.be> Message-ID: Nick, If you have simple X,Y coordinate data, could I suggest Grace? http://plasma-gate.weizmann.ac.il/Grace/ Regards, Tony P. > -----Original Message----- > From: emboss-bounces at lists.open-bio.org [mailto:emboss- > bounces at lists.open-bio.org] On Behalf Of Guy Bottu > Sent: 30 May 2008 09:55 > To: Staffa, Nick (NIH/NIEHS) > Cc: Rodgers, Gary (NIH/NIEHS) [C]; Young,Reeves (NIH/NIEHS) [C]; > emboss at lists.open-bio.org > Subject: Re: [EMBOSS] Dot Plot > > Staffa, Nick (NIH/NIEHS) wrote: > > After a day of futzing around trying to create the point file that > GCG's > > Compare makes, with an whole page of Perl, I attacked the figure file > it > > makes. If one doesnt care about axes, then 2 or 3 commands set up the > window > > and one adds his points in the original units - a half page of perl. > > Figure is a great program. It's so old that surely they could open > source > > it. > > That has been discussed a lot these days. Since they have abandonned > the idea of > making cash from it, why could they not make the very useful SeqLab or > even all > their software OpenSource ? But anyway, there is the GCGfigure program > that runs > on old MacOS and has always been freeware. > > Guy > > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss