From felipe.egrupos at gmail.com Sat Oct 2 12:01:33 2010 From: felipe.egrupos at gmail.com (=?UTF-8?B?RmVsaXBlIE1hcnTDrW5lei1QYXN0b3I=?=) Date: Sat, 02 Oct 2010 18:01:33 +0200 Subject: [EMBOSS] problems with eprimer3 Message-ID: <4CA7575D.70803@gmail.com> Dear EMBOSS developers and users, I am having some problems with the eprimer3 application in EMBOSS. I have been using primer3 online (primer3plus, ncbi site) with good results, and I just tried using it in EMBOSS. I am using MacOS 10.6.4 (Snow Leopard), with EMBOSS 6.3.1 installed by Fink (an UNIX porting system for MacOS). The primer3 version is 2.2.3. One of the problems has already being described in this list, but it seems to still be around. When I call eprimer3 with a sequence, the output is: Picks PCR primers and hybridization oligos Error: Missing SEQUENCE tag See this thread for details, I did the same tests and the results were similar; primer3_core is OK, but it seems that eprimer3 has not been updated yet to successfully communicate with the primer3_core 2.x versions: http://www.mail-archive.com/emboss at lists.open-bio.org/msg01405.html I have not tried yet the developer's version of EMBOSS, should I? Regards, -- --------------------oOo-------------------- Felipe Mart?nez-Pastor, Ph. D. ITRA-ULE (Research in Assisted Reproductive Technologies) INDEGSAL (edificio Biomedicina) University of Le?n Campus de Vegazana 24071-Le?n (Spain) Office phone: +34 987 291 000 + 5679 Fax: +34 987 291 282 Mobile: +34 687 365 362 e-mail: felipe.martinez at unileon.es f.martinez.pastor at gmail.com website: http://itra.unileon.es ------------------------------------------- From ajb at ebi.ac.uk Sat Oct 2 13:22:55 2010 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Sat, 2 Oct 2010 18:22:55 +0100 (BST) Subject: [EMBOSS] problems with eprimer3 In-Reply-To: <4CA7575D.70803@gmail.com> References: <4CA7575D.70803@gmail.com> Message-ID: <45693.86.26.12.63.1286040175.squirrel@webmail.ebi.ac.uk> Hello Felipe, Thanks for the reminder of this. Downloading the developer's version will not help. A version of eprimer3 that should work with primer3 2.x.x can be downloaded from: http://www.ebi.ac.uk/~ajb/eprimer3/eprimer3.c if you're desperate. Note that it hasn't been tested very recently and is not, as yet, official. We are still debating how to deal with new and old versions of primer3. An odd hindrance is, given that it would be useful to keep the 1.x.x version around for compatibility reasons, what to call them. If you choose to try the above then any feedback would be welcome. ATB Alan > Dear EMBOSS developers and users, > > I am having some problems with the eprimer3 application in EMBOSS. I > have been using primer3 online (primer3plus, ncbi site) with good > results, and I just tried using it in EMBOSS. I am using MacOS 10.6.4 > (Snow Leopard), with EMBOSS 6.3.1 installed by Fink (an UNIX porting > system for MacOS). The primer3 version is 2.2.3. > > One of the problems has already being described in this list, but it > seems to still be around. When I call eprimer3 with a sequence, the > output is: > Picks PCR primers and hybridization oligos > Error: Missing SEQUENCE tag > > See this thread for details, I did the same tests and the results were > similar; primer3_core is OK, but it seems that eprimer3 has not been > updated yet to successfully communicate with the primer3_core 2.x > versions: > http://www.mail-archive.com/emboss at lists.open-bio.org/msg01405.html > > I have not tried yet the developer's version of EMBOSS, should I? > > Regards, > > -- > --------------------oOo-------------------- > Felipe Mart??nez-Pastor, Ph. D. > ITRA-ULE (Research in Assisted Reproductive Technologies) > INDEGSAL (edificio Biomedicina) > University of Le??n > Campus de Vegazana > 24071-Le??n (Spain) > Office phone: +34 987 291 000 + 5679 > Fax: +34 987 291 282 > Mobile: +34 687 365 362 > e-mail: felipe.martinez at unileon.es > f.martinez.pastor at gmail.com > website: http://itra.unileon.es > ------------------------------------------- > > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > From felipe.egrupos at gmail.com Sat Oct 2 19:45:13 2010 From: felipe.egrupos at gmail.com (=?ISO-8859-1?Q?Felipe_Mart=EDnez-Pastor?=) Date: Sun, 03 Oct 2010 01:45:13 +0200 Subject: [EMBOSS] problems with eprimer3 In-Reply-To: <45693.86.26.12.63.1286040175.squirrel@webmail.ebi.ac.uk> References: <4CA7575D.70803@gmail.com> <45693.86.26.12.63.1286040175.squirrel@webmail.ebi.ac.uk> Message-ID: <4CA7C409.6090000@gmail.com> I replaced the eprimer3.c from EMBOSS 6.3.1, complied and, worked! Thank you for the help. It is a tricky decision. By now, I suggest adding a warning in the eprimer3 manual page? Regards, Felipe El 02/10/10 19:22, ajb at ebi.ac.uk escribi?: > Hello Felipe, > > Thanks for the reminder of this. Downloading the developer's version > will not help. > > A version of eprimer3 that should work with primer3 2.x.x can > be downloaded from: > > http://www.ebi.ac.uk/~ajb/eprimer3/eprimer3.c > > if you're desperate. Note that it hasn't been tested very recently and is > not, as yet, official. We are still debating how to deal with > new and old versions of primer3. An odd hindrance > is, given that it would be useful to keep the > 1.x.x version around for compatibility reasons, what to call them. > > If you choose to try the above then any feedback would be welcome. > > ATB > > Alan > > > >> Dear EMBOSS developers and users, >> >> I am having some problems with the eprimer3 application in EMBOSS. I >> have been using primer3 online (primer3plus, ncbi site) with good >> results, and I just tried using it in EMBOSS. I am using MacOS 10.6.4 >> (Snow Leopard), with EMBOSS 6.3.1 installed by Fink (an UNIX porting >> system for MacOS). The primer3 version is 2.2.3. >> >> One of the problems has already being described in this list, but it >> seems to still be around. When I call eprimer3 with a sequence, the >> output is: >> Picks PCR primers and hybridization oligos >> Error: Missing SEQUENCE tag >> >> See this thread for details, I did the same tests and the results were >> similar; primer3_core is OK, but it seems that eprimer3 has not been >> updated yet to successfully communicate with the primer3_core 2.x >> versions: >> http://www.mail-archive.com/emboss at lists.open-bio.org/msg01405.html >> >> I have not tried yet the developer's version of EMBOSS, should I? >> >> Regards, >> >> -- >> --------------------oOo-------------------- >> Felipe Mart??nez-Pastor, Ph. D. >> ITRA-ULE (Research in Assisted Reproductive Technologies) >> INDEGSAL (edificio Biomedicina) >> University of Le??n >> Campus de Vegazana >> 24071-Le??n (Spain) >> Office phone: +34 987 291 000 + 5679 >> Fax: +34 987 291 282 >> Mobile: +34 687 365 362 >> e-mail: felipe.martinez at unileon.es >> f.martinez.pastor at gmail.com >> website: http://itra.unileon.es >> ------------------------------------------- >> >> _______________________________________________ >> EMBOSS mailing list >> EMBOSS at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/emboss >> > > > From bcitron at health.usf.edu Fri Oct 8 13:31:41 2010 From: bcitron at health.usf.edu (Citron, Bruce) Date: Fri, 8 Oct 2010 13:31:41 -0400 Subject: [EMBOSS] Restrict- exclude range Message-ID: Is there a way to list restriction enzyme sites that cut within one region but also do not cut within another region with the EMBOSS programs? I thought that restrict should be able to do this, but it doesn't seem to or I'm missing something. GCG's mapsort -excl does this. Thanks, Bruce -- Bruce A. Citron, Ph.D., Bay Pines VA From jison at ebi.ac.uk Tue Oct 12 08:10:09 2010 From: jison at ebi.ac.uk (Jon Ison) Date: Tue, 12 Oct 2010 13:10:09 +0100 (BST) Subject: [EMBOSS] Restrict- exclude range In-Reply-To: References: Message-ID: <51287.172.22.100.208.1286885409.squirrel@webmail.ebi.ac.uk> Hi Bruce I think the short answer is "no", at least not directly. We'll add it to the list of things to do. Cheers Jon > Is there a way to list restriction enzyme sites that cut within one region but also do not cut > within another region with the EMBOSS programs? > I thought that restrict should be able to do this, but it doesn't seem to or I'm missing > something. GCG's mapsort -excl does this. > Thanks, > Bruce > -- > Bruce A. Citron, Ph.D., Bay Pines VA > > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > From bcitron at health.usf.edu Tue Oct 12 12:23:49 2010 From: bcitron at health.usf.edu (Citron, Bruce) Date: Tue, 12 Oct 2010 12:23:49 -0400 Subject: [EMBOSS] Restrict- exclude range In-Reply-To: <51287.172.22.100.208.1286885409.squirrel@webmail.ebi.ac.uk> Message-ID: Jon- Your point about "not directly" inspired me to generate an alias in a .src file. If one keeps a list of favorite restriction enzymes in a file called lmbenz.dat (containing one restriction enzyme name per line) in a directory like ~/sequences, then the command: re t.gbk 300 500 Will generate restrict output only showing enzymes that do not cut within the region 300 to 500 in the sequence named as the first parameter, t.gbk in this case. alias re 'restrict -auto \!:1 re.tmp -enz=@~bcitron/sequences/lmbenz.dat -sb \!:2 -sen \!:3 -rformat2 simple; grep name re.tmp| sed s/"Enzyme_name: "//g > rel.tmp; grep -v -f rel.tmp ~bcitron/sequences/lmbenz.dat > rene.dat; restrict -auto \!:1 stdout -enz=@rene.dat' There are probably better ways to accomplish this, and with intermediate files, one should be able to show the excluded enzymes and other enzyme sets. And there may be output options for restrict that don't require quite the grep and sed cleanup. Also, it should certainly be possible to adjust this for multiple exclusion ranges, etc. Thanks, Bruce From benys at usp.br Thu Oct 14 11:39:30 2010 From: benys at usp.br (Beny Spira) Date: Thu, 14 Oct 2010 12:39:30 -0300 Subject: [EMBOSS] jemboss installation Message-ID: Hi I used to have Jemboss installed and running smoothly in my computer. I had to install it again (from emboss 6.1.0), but every time I run ./runJemboss.sh I get the following mesage: Trying to install again a standalone Exception in thread "main" java.lang.NoClassDefFoundError: org/emboss/jemboss/Jemboss Caused by: java.lang.ClassNotFoundException: org.emboss.jemboss.Jemboss at java.net.URLClassLoader$1.run(URLClassLoader.java:202) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(URLClassLoader.java:190) at java.lang.ClassLoader.loadClass(ClassLoader.java:307) at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301) at java.lang.ClassLoader.loadClass(ClassLoader.java:248) Could not find the main class: org.emboss.jemboss.Jemboss. Program will exit. The version of Java installed is java-6-sun-1.6.0.20 Any help would be appreciated, Beny -- Beny Spira Departamento de Microbiologia Instituto de Ci?ncias Biom?dicas Universidade de S?o Paulo Av. Prof. Lineu Prestes 1374 S?o Paulo-SP CEP:05508-900 Brasil Tel: 5511-3091-7347 FAX: 5511-3091-7354 E-mail: benys at usp.br Homepage: www.icb.usp.br/~benys From felipe.egrupos at gmail.com Sat Oct 2 16:01:33 2010 From: felipe.egrupos at gmail.com (=?UTF-8?B?RmVsaXBlIE1hcnTDrW5lei1QYXN0b3I=?=) Date: Sat, 02 Oct 2010 18:01:33 +0200 Subject: [EMBOSS] problems with eprimer3 Message-ID: <4CA7575D.70803@gmail.com> Dear EMBOSS developers and users, I am having some problems with the eprimer3 application in EMBOSS. I have been using primer3 online (primer3plus, ncbi site) with good results, and I just tried using it in EMBOSS. I am using MacOS 10.6.4 (Snow Leopard), with EMBOSS 6.3.1 installed by Fink (an UNIX porting system for MacOS). The primer3 version is 2.2.3. One of the problems has already being described in this list, but it seems to still be around. When I call eprimer3 with a sequence, the output is: Picks PCR primers and hybridization oligos Error: Missing SEQUENCE tag See this thread for details, I did the same tests and the results were similar; primer3_core is OK, but it seems that eprimer3 has not been updated yet to successfully communicate with the primer3_core 2.x versions: http://www.mail-archive.com/emboss at lists.open-bio.org/msg01405.html I have not tried yet the developer's version of EMBOSS, should I? Regards, -- --------------------oOo-------------------- Felipe Mart?nez-Pastor, Ph. D. ITRA-ULE (Research in Assisted Reproductive Technologies) INDEGSAL (edificio Biomedicina) University of Le?n Campus de Vegazana 24071-Le?n (Spain) Office phone: +34 987 291 000 + 5679 Fax: +34 987 291 282 Mobile: +34 687 365 362 e-mail: felipe.martinez at unileon.es f.martinez.pastor at gmail.com website: http://itra.unileon.es ------------------------------------------- From ajb at ebi.ac.uk Sat Oct 2 17:22:55 2010 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Sat, 2 Oct 2010 18:22:55 +0100 (BST) Subject: [EMBOSS] problems with eprimer3 In-Reply-To: <4CA7575D.70803@gmail.com> References: <4CA7575D.70803@gmail.com> Message-ID: <45693.86.26.12.63.1286040175.squirrel@webmail.ebi.ac.uk> Hello Felipe, Thanks for the reminder of this. Downloading the developer's version will not help. A version of eprimer3 that should work with primer3 2.x.x can be downloaded from: http://www.ebi.ac.uk/~ajb/eprimer3/eprimer3.c if you're desperate. Note that it hasn't been tested very recently and is not, as yet, official. We are still debating how to deal with new and old versions of primer3. An odd hindrance is, given that it would be useful to keep the 1.x.x version around for compatibility reasons, what to call them. If you choose to try the above then any feedback would be welcome. ATB Alan > Dear EMBOSS developers and users, > > I am having some problems with the eprimer3 application in EMBOSS. I > have been using primer3 online (primer3plus, ncbi site) with good > results, and I just tried using it in EMBOSS. I am using MacOS 10.6.4 > (Snow Leopard), with EMBOSS 6.3.1 installed by Fink (an UNIX porting > system for MacOS). The primer3 version is 2.2.3. > > One of the problems has already being described in this list, but it > seems to still be around. When I call eprimer3 with a sequence, the > output is: > Picks PCR primers and hybridization oligos > Error: Missing SEQUENCE tag > > See this thread for details, I did the same tests and the results were > similar; primer3_core is OK, but it seems that eprimer3 has not been > updated yet to successfully communicate with the primer3_core 2.x > versions: > http://www.mail-archive.com/emboss at lists.open-bio.org/msg01405.html > > I have not tried yet the developer's version of EMBOSS, should I? > > Regards, > > -- > --------------------oOo-------------------- > Felipe Mart??nez-Pastor, Ph. D. > ITRA-ULE (Research in Assisted Reproductive Technologies) > INDEGSAL (edificio Biomedicina) > University of Le??n > Campus de Vegazana > 24071-Le??n (Spain) > Office phone: +34 987 291 000 + 5679 > Fax: +34 987 291 282 > Mobile: +34 687 365 362 > e-mail: felipe.martinez at unileon.es > f.martinez.pastor at gmail.com > website: http://itra.unileon.es > ------------------------------------------- > > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > From felipe.egrupos at gmail.com Sat Oct 2 23:45:13 2010 From: felipe.egrupos at gmail.com (=?ISO-8859-1?Q?Felipe_Mart=EDnez-Pastor?=) Date: Sun, 03 Oct 2010 01:45:13 +0200 Subject: [EMBOSS] problems with eprimer3 In-Reply-To: <45693.86.26.12.63.1286040175.squirrel@webmail.ebi.ac.uk> References: <4CA7575D.70803@gmail.com> <45693.86.26.12.63.1286040175.squirrel@webmail.ebi.ac.uk> Message-ID: <4CA7C409.6090000@gmail.com> I replaced the eprimer3.c from EMBOSS 6.3.1, complied and, worked! Thank you for the help. It is a tricky decision. By now, I suggest adding a warning in the eprimer3 manual page? Regards, Felipe El 02/10/10 19:22, ajb at ebi.ac.uk escribi?: > Hello Felipe, > > Thanks for the reminder of this. Downloading the developer's version > will not help. > > A version of eprimer3 that should work with primer3 2.x.x can > be downloaded from: > > http://www.ebi.ac.uk/~ajb/eprimer3/eprimer3.c > > if you're desperate. Note that it hasn't been tested very recently and is > not, as yet, official. We are still debating how to deal with > new and old versions of primer3. An odd hindrance > is, given that it would be useful to keep the > 1.x.x version around for compatibility reasons, what to call them. > > If you choose to try the above then any feedback would be welcome. > > ATB > > Alan > > > >> Dear EMBOSS developers and users, >> >> I am having some problems with the eprimer3 application in EMBOSS. I >> have been using primer3 online (primer3plus, ncbi site) with good >> results, and I just tried using it in EMBOSS. I am using MacOS 10.6.4 >> (Snow Leopard), with EMBOSS 6.3.1 installed by Fink (an UNIX porting >> system for MacOS). The primer3 version is 2.2.3. >> >> One of the problems has already being described in this list, but it >> seems to still be around. When I call eprimer3 with a sequence, the >> output is: >> Picks PCR primers and hybridization oligos >> Error: Missing SEQUENCE tag >> >> See this thread for details, I did the same tests and the results were >> similar; primer3_core is OK, but it seems that eprimer3 has not been >> updated yet to successfully communicate with the primer3_core 2.x >> versions: >> http://www.mail-archive.com/emboss at lists.open-bio.org/msg01405.html >> >> I have not tried yet the developer's version of EMBOSS, should I? >> >> Regards, >> >> -- >> --------------------oOo-------------------- >> Felipe Mart??nez-Pastor, Ph. D. >> ITRA-ULE (Research in Assisted Reproductive Technologies) >> INDEGSAL (edificio Biomedicina) >> University of Le??n >> Campus de Vegazana >> 24071-Le??n (Spain) >> Office phone: +34 987 291 000 + 5679 >> Fax: +34 987 291 282 >> Mobile: +34 687 365 362 >> e-mail: felipe.martinez at unileon.es >> f.martinez.pastor at gmail.com >> website: http://itra.unileon.es >> ------------------------------------------- >> >> _______________________________________________ >> EMBOSS mailing list >> EMBOSS at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/emboss >> > > > From bcitron at health.usf.edu Fri Oct 8 17:31:41 2010 From: bcitron at health.usf.edu (Citron, Bruce) Date: Fri, 8 Oct 2010 13:31:41 -0400 Subject: [EMBOSS] Restrict- exclude range Message-ID: Is there a way to list restriction enzyme sites that cut within one region but also do not cut within another region with the EMBOSS programs? I thought that restrict should be able to do this, but it doesn't seem to or I'm missing something. GCG's mapsort -excl does this. Thanks, Bruce -- Bruce A. Citron, Ph.D., Bay Pines VA From jison at ebi.ac.uk Tue Oct 12 12:10:09 2010 From: jison at ebi.ac.uk (Jon Ison) Date: Tue, 12 Oct 2010 13:10:09 +0100 (BST) Subject: [EMBOSS] Restrict- exclude range In-Reply-To: References: Message-ID: <51287.172.22.100.208.1286885409.squirrel@webmail.ebi.ac.uk> Hi Bruce I think the short answer is "no", at least not directly. We'll add it to the list of things to do. Cheers Jon > Is there a way to list restriction enzyme sites that cut within one region but also do not cut > within another region with the EMBOSS programs? > I thought that restrict should be able to do this, but it doesn't seem to or I'm missing > something. GCG's mapsort -excl does this. > Thanks, > Bruce > -- > Bruce A. Citron, Ph.D., Bay Pines VA > > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > From bcitron at health.usf.edu Tue Oct 12 16:23:49 2010 From: bcitron at health.usf.edu (Citron, Bruce) Date: Tue, 12 Oct 2010 12:23:49 -0400 Subject: [EMBOSS] Restrict- exclude range In-Reply-To: <51287.172.22.100.208.1286885409.squirrel@webmail.ebi.ac.uk> Message-ID: Jon- Your point about "not directly" inspired me to generate an alias in a .src file. If one keeps a list of favorite restriction enzymes in a file called lmbenz.dat (containing one restriction enzyme name per line) in a directory like ~/sequences, then the command: re t.gbk 300 500 Will generate restrict output only showing enzymes that do not cut within the region 300 to 500 in the sequence named as the first parameter, t.gbk in this case. alias re 'restrict -auto \!:1 re.tmp -enz=@~bcitron/sequences/lmbenz.dat -sb \!:2 -sen \!:3 -rformat2 simple; grep name re.tmp| sed s/"Enzyme_name: "//g > rel.tmp; grep -v -f rel.tmp ~bcitron/sequences/lmbenz.dat > rene.dat; restrict -auto \!:1 stdout -enz=@rene.dat' There are probably better ways to accomplish this, and with intermediate files, one should be able to show the excluded enzymes and other enzyme sets. And there may be output options for restrict that don't require quite the grep and sed cleanup. Also, it should certainly be possible to adjust this for multiple exclusion ranges, etc. Thanks, Bruce From benys at usp.br Thu Oct 14 15:39:30 2010 From: benys at usp.br (Beny Spira) Date: Thu, 14 Oct 2010 12:39:30 -0300 Subject: [EMBOSS] jemboss installation Message-ID: Hi I used to have Jemboss installed and running smoothly in my computer. I had to install it again (from emboss 6.1.0), but every time I run ./runJemboss.sh I get the following mesage: Trying to install again a standalone Exception in thread "main" java.lang.NoClassDefFoundError: org/emboss/jemboss/Jemboss Caused by: java.lang.ClassNotFoundException: org.emboss.jemboss.Jemboss at java.net.URLClassLoader$1.run(URLClassLoader.java:202) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(URLClassLoader.java:190) at java.lang.ClassLoader.loadClass(ClassLoader.java:307) at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301) at java.lang.ClassLoader.loadClass(ClassLoader.java:248) Could not find the main class: org.emboss.jemboss.Jemboss. Program will exit. The version of Java installed is java-6-sun-1.6.0.20 Any help would be appreciated, Beny -- Beny Spira Departamento de Microbiologia Instituto de Ci?ncias Biom?dicas Universidade de S?o Paulo Av. Prof. Lineu Prestes 1374 S?o Paulo-SP CEP:05508-900 Brasil Tel: 5511-3091-7347 FAX: 5511-3091-7354 E-mail: benys at usp.br Homepage: www.icb.usp.br/~benys