From newsletter at prographicssportswear.com Thu Feb 5 12:36:34 2004 From: newsletter at prographicssportswear.com (newsletter at prographicssportswear.com) Date: Thu, 5 Feb 2004 12:36:34 -0500 Subject: Please send this email to your T-shirt ordering committee Message-ID: <200402051736.i15HaYT08268@www.prographicssportswear.com> You must use an HTML compliant e-mail client to view this message properly. Visit http://www.prographicssportswear.com for more information. ------------- Click the link to unsubscribe: http://news.prographicssportswear.com/submit.php?id=27&le_email=emboss-dev at embnet.org -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.open-bio.org/pipermail/emboss-dev/attachments/20040205/41810eda/attachment.html From d.counsell at rfcgr.mrc.ac.uk Tue Feb 10 12:32:16 2004 From: d.counsell at rfcgr.mrc.ac.uk (Damian Counsell) Date: Tue, 10 Feb 2004 17:32:16 +0000 Subject: the Matrix (reloaded) Message-ID: <20040210173216.GF26975@dev4.hgmp.mrc.ac.uk> EMBOSSnians! Did anyone get around to writing something to write scoring matrices (corresponding to the existing functions to read matrices)? ajMatrixRead --> ajMatrixWrite ajMatrixfRead --> ajMatrixfWrite all the best Damian -- MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SB, UK phone: +44 (0)1223 494585 fax: +44 (0)1223 494512 email: d.counsell at hgmp.mrc.ac.uk Web: http://www.rfcgr.mrc.ac.uk/~dcounsel/ From gbottu at ben.vub.ac.be Fri Feb 13 06:46:56 2004 From: gbottu at ben.vub.ac.be (Guy Bottu) Date: Fri, 13 Feb 2004 12:46:56 +0100 Subject: remarks about sequence formats Message-ID: <20040213114656.GA26101@bigben.ulb.ac.be> Dear developers, I just installed EMBOSS 2.8.0 at the BEN site. I did some testing and I noticed the following things about file formats : - the documentation says that "phylip" is non-interleaved format and "phylip3" interleaved format, but the programs write exactly the reverse ("phylip3::myseqs" has the sequences the one after the other and "phylip::myseqs" has them interleaved) - PAUP format is always written with "datatype=DNA", also when the sequences are proteins - an old pain in the ass : Staden "experiment" format is still not handled. I include an "experiment" file as attachment. As far as I know the differences with EMBL format are : - more field types - AC not mandatory - only 1 sequence per file - data fields allowed behind the sequence Note the AV lines with the "confidence values" of the bases. EMBOSS library routines to read and write these could be useful. There is software that can do something intelligent with "confidence values", e.g. Primer3, but at the present eprimer3 cannot handle them. Regards, Guy Bottu -------------- next part -------------- ID 000256_11cR EN 000256_11cR LN 000256_11cR..ztr LT ZTR AQ 50.180000 AV 18 20 18 18 19 13 13 6 6 6 6 6 9 7 8 11 11 21 24 32 39 46 40 AV 33 34 29 29 29 26 20 20 26 22 26 42 46 51 51 45 40 32 32 AV 32 33 34 32 24 17 13 10 10 19 19 28 28 28 29 35 35 40 39 AV 51 51 51 46 46 42 42 42 46 46 51 51 56 56 51 51 51 51 46 AV 40 35 35 35 39 39 39 56 51 51 51 51 39 39 39 39 39 39 45 AV 40 45 45 45 51 51 51 51 51 51 51 45 45 45 45 51 51 56 56 AV 51 51 51 51 51 51 56 56 56 56 56 56 56 56 56 56 56 51 51 AV 51 51 45 45 51 51 51 40 51 51 45 45 45 40 40 43 43 43 43 AV 45 51 45 56 51 51 51 51 51 45 45 45 45 45 45 51 51 51 51 AV 45 45 51 51 51 51 56 56 56 56 56 56 51 51 51 51 51 56 56 AV 56 51 51 51 51 51 51 56 56 56 56 56 56 56 56 46 43 43 43 AV 43 43 43 51 43 43 43 43 43 43 56 56 56 56 56 56 56 56 56 AV 56 56 51 45 45 45 45 45 51 51 51 51 51 56 56 51 56 56 51 AV 51 51 51 51 51 51 56 56 56 56 51 51 51 51 51 51 56 51 51 AV 51 51 51 51 56 56 56 56 56 51 51 51 51 51 51 51 51 56 56 AV 56 56 56 56 56 45 45 45 43 43 43 46 46 46 51 56 56 56 51 AV 51 51 56 56 45 45 45 45 45 45 56 56 56 56 56 56 56 56 56 AV 51 51 51 51 51 51 43 43 43 43 43 43 43 45 45 45 45 45 46 AV 43 43 43 43 43 43 51 56 43 43 43 43 43 43 51 51 46 46 46 AV 46 51 46 51 51 51 51 51 51 56 56 56 51 45 45 45 45 45 45 AV 51 51 51 56 51 51 51 51 51 51 51 56 56 56 56 56 56 51 51 AV 45 45 45 45 45 45 51 51 56 56 56 56 56 56 56 56 56 56 56 AV 56 51 51 51 45 45 45 45 45 45 43 43 43 43 43 43 43 43 43 AV 46 46 51 41 40 45 45 45 45 51 51 45 51 51 45 45 45 45 45 AV 45 45 45 45 45 45 45 45 45 51 56 56 56 56 56 56 56 56 56 AV 56 51 51 51 45 45 45 40 40 37 37 37 40 56 51 56 56 56 51 AV 51 51 51 51 51 56 45 45 45 45 40 40 45 45 40 40 45 45 40 AV 40 45 45 51 51 51 51 46 46 40 51 40 37 37 37 40 45 45 45 AV 45 56 45 40 35 35 35 32 32 35 46 42 51 51 51 46 46 37 35 AV 35 35 35 39 40 40 40 35 35 35 35 35 35 42 42 46 46 46 40 AV 40 40 40 40 38 42 42 27 19 11 11 11 28 27 40 40 40 44 32 AV 32 29 29 15 20 18 24 14 19 9 10 10 19 27 37 25 25 25 24 AV 29 29 29 20 12 12 13 12 15 12 11 8 8 8 8 7 7 7 4 0 0 0 AV 0 0 0 0 0 SQ GTGGGCAGAA AAGTTGACAT TCCTCTTCTG CATTTCCTGG ATTGAAAACA GAGCAAATGA CTGGCGCTTT GAAACCTTGA ATGTATTCTG CAAATACTGA GCATCAAGTT CACTTTCTTC CATTTCTATG CTTGTTTCCC GACTGTGGTT AACTTCATGT CCCAATGGAT ACTTAAAGCC TTCTGTGTCA TTTCTATTAT CTTTGGAACA ACCATGAATT AGTCCCTTGG GGTTTTCAAA TGCTGCACAC TGACTCACAC ATTTATTTGG TTCTGTTTTT GCCTTCCCTA GAGTGCTAAC TTCCAGTAAC GAGATACTTT CCTGAGTGCC ATAATCAGTA CCAGGTACCA GTGAAATACT GCTACTCTCT ACAGATCTTT CAGTTTGCAA AACCCTTTCT CCACTTAACA TGAGATCTTT GGGGTCTTCA GCATTATTAG ACACTTTAAC TGTTTCTAGT TTCTCTTCTT TTTCTTCTCT TGGAAGGCTA GGATTGACAA ATTCTTTAAG TTCACTGGTA TTTGAACACT TAGTAAAAGA ACCAGGTGCA TTTGTTAACT TCAGCTCTGG GAAAGTATCA CTGTCATGTC TTTTACTTGT CTGTTCATTT GGCACTGGCC GTCGCGCTTC ANNNNNNNN // TN 000256_11c PR 2 QL 17 QR 617 WT /home/gbottu/demo/exercise_snip/000906_11cR.scf WL -1 WR -1 TG MUTA - 50..50 TG C->T Sensitivity= 7.86, Alignment=0.14, Width=0.86, Amplitude=643 TG MUTA - 351..351 TG T->C Sensitivity= 8.13, Alignment=0.07, Width=1.00, Amplitude=1105 TG MUTA - 580..580 TG C->T Sensitivity= 6.19, Alignment=0.29, Width=1.21, Amplitude=1338 TG HETE - 585..585 TG AG Ratio=0.87, Alignment=0.00, Amplitude1=0.18, Amplitude2=0.15 From pmr at ebi.ac.uk Fri Feb 13 06:49:28 2004 From: pmr at ebi.ac.uk (Peter Rice) Date: Fri, 13 Feb 2004 11:49:28 +0000 Subject: remarks about sequence formats In-Reply-To: <20040213114656.GA26101@bigben.ulb.ac.be> References: <20040213114656.GA26101@bigben.ulb.ac.be> Message-ID: <402CB9C8.9050708@ebi.ac.uk> Guy Bottu wrote: > Dear developers, > > I just installed EMBOSS 2.8.0 at the BEN site. I did some testing and I > noticed the following things about file formats : Many thanks. There are also some problems with Nexus files for unaligned sequences, to be fixed in 2.8.1 regards, Peter From gbottu at ben.vub.ac.be Fri Feb 13 15:16:57 2004 From: gbottu at ben.vub.ac.be (Guy Bottu) Date: Fri, 13 Feb 2004 21:16:57 +0100 Subject: Staden and EMBOSS 2.8.O Message-ID: <20040213201657.GB29575@bigben.ulb.ac.be> Dear colleagues, As you all know, with EMBOSS 2.8.O the syntax of the ACD files has changed. An unfortunate consequence is that EMBOSS programs do not work well or not at all anymore under Staden spin or spin2. The script acd2tcl.tcl should be updated as to handle new things like the rename required -> standard and the use of $acdprotein. Unfortunately there is no support for Staden anymore (well, it was recently announced that James Bonfield is working at Sanger Centre, but according to the Web page he is only developing gap4, not spin). Does someone know more about it ? Guy Bottu, BEN From d.counsell at rfcgr.mrc.ac.uk Tue Feb 17 09:54:51 2004 From: d.counsell at rfcgr.mrc.ac.uk (Damian Counsell) Date: Tue, 17 Feb 2004 14:54:51 +0000 Subject: EMBOSS/Jemboss mentioned on Slashdot Message-ID: <20040217145451.GD1977@dev4.hgmp.mrc.ac.uk> EMBOSSnians! I am a pretty infrequent Slashdot reader these days so I've only just noticed that an article about BioKnoppix---featuring EMBOSS and Jemboss very prominently---appeared on /. this Saturday just gone: http://slashdot.org/article.pl?sid=04/02/14/188237 . In fact, it's so long since I visited there that I have moderator access. I feel one of my Alastair Campbell moments coming on. (If only some of the commenters were actually talking about the story itself so I could spin the debate in EMBOSS's favour properly.) all the best Damian -- MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SB, UK phone: +44 (0)1223 494585 fax: +44 (0)1223 494512 email: d.counsell at hgmp.mrc.ac.uk Web: http://www.rfcgr.mrc.ac.uk/~dcounsel/ From pmr at ebi.ac.uk Mon Feb 23 05:22:37 2004 From: pmr at ebi.ac.uk (Peter Rice) Date: Mon, 23 Feb 2004 10:22:37 +0000 Subject: [EMBOSS] Staden and EMBOSS 2.8.O In-Reply-To: <2DC41140A89ED411989D00508BDCD9ED01E28CD0@bi-exsrv1.iapc.bbsrc.ac.uk> References: <2DC41140A89ED411989D00508BDCD9ED01E28CD0@bi-exsrv1.iapc.bbsrc.ac.uk> Message-ID: <4039D46D.6000305@ebi.ac.uk> simon andrews (BI) wrote: > >>-----Original Message----- >>From: Guy Bottu [mailto:gbottu at ben.vub.ac.be] >>Subject: [EMBOSS] Staden and EMBOSS 2.8.O >> >>Unfortunately there is no support for Staden anymore (well, >>it was recently announced that James Bonfield is working >>at Sanger Centre, but according to the Web page he is >>only developing gap4, not spin). Does someone know more about it ? > > > James recently announced that the MRC have finally agreed to release Staden under an opensource licence. It is therefore now being hosted and developed as a sourceforge project: > > http://staden.sourceforge.net/ > > https://sourceforge.net/projects/staden > > ..therefore if you're up to making the changes yourself you can submit patches to the project, or if not you can file it as a bug which someone else will hopefully pick up. I have updated EMBSOS in the past to produce graphics in SPIN for some proggrams that did not do it "normally". I recently volunteered to update SPIN for EMBOSS 2.8.1 (due out soon) and will put the updates on the Staden SourceForge site and into the EMBOSS distribution. James Bonfield is here on campus so we can easily coordinate this. I may have a volunteer to test the SPIN/EMBOSS interface - but more would be welcome! regards, Peter Rice From pmr at ebi.ac.uk Mon Feb 23 05:37:51 2004 From: pmr at ebi.ac.uk (Peter Rice) Date: Mon, 23 Feb 2004 10:37:51 +0000 Subject: Staden and EMBOSS 2.8.O Message-ID: <4039D7FF.8000404@ebi.ac.uk> simon andrews (BI) wrote: > >>-----Original Message----- >>From: Guy Bottu [mailto:gbottu at ben.vub.ac.be] >>Subject: [EMBOSS] Staden and EMBOSS 2.8.O >> >>Unfortunately there is no support for Staden anymore (well, >>it was recently announced that James Bonfield is working >>at Sanger Centre, but according to the Web page he is >>only developing gap4, not spin). Does someone know more about it ? > > > James recently announced that the MRC have finally agreed to release Staden under an opensource licence. It is therefore now being hosted and developed as a sourceforge project: > > http://staden.sourceforge.net/ > > https://sourceforge.net/projects/staden > > ..therefore if you're up to making the changes yourself you can submit patches to the project, or if not you can file it as a bug which someone else will hopefully pick up. I have updated EMBOSS in the past to produce graphics in SPIN for some programs that did not do it "normally". I recently volunteered to update SPIN for EMBOSS 2.8.1 (due out soon) and will put the updates on the Staden SourceForge site and into the EMBOSS distribution. James Bonfield is here on campus so we can easily coordinate this. I may have a volunteer to test the SPIN/EMBOSS interface - but more would be welcome! regards, Peter Rice From gbottu at ben.vub.ac.be Thu Feb 26 06:04:16 2004 From: gbottu at ben.vub.ac.be (Guy Bottu) Date: Thu, 26 Feb 2004 12:04:16 +0100 Subject: The empty file problem Message-ID: <20040226110416.GA29428@bigben.ulb.ac.be> from : BEN Dear developers, Can I point your attention to a (minor) problem ? When you run e.g. the program charge on sw:papa_carpa it creates a file papa_carpa.charge. If you run it with parameter -plot it will create a graphic but it will also create an empty file papa_carpa.charge. If a papa_carpa.charge from a previous run existed already it is overwritten. Wouldn't it be appropriate to add to : outfile: outfile [ standard: "@(!$(plot))" knowntype: "charge output" ] a line : nullok: "$(plot)" The same problem also exists for dan, findk, freak, hmoment, iep, syco and tcode. Regards, Guy Bottu From newsletter at prographicssportswear.com Thu Feb 5 17:36:34 2004 From: newsletter at prographicssportswear.com (newsletter at prographicssportswear.com) Date: Thu, 5 Feb 2004 12:36:34 -0500 Subject: Please send this email to your T-shirt ordering committee Message-ID: <200402051736.i15HaYT08268@www.prographicssportswear.com> You must use an HTML compliant e-mail client to view this message properly. Visit http://www.prographicssportswear.com for more information. ------------- Click the link to unsubscribe: http://news.prographicssportswear.com/submit.php?id=27&le_email=emboss-dev at embnet.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From d.counsell at rfcgr.mrc.ac.uk Tue Feb 10 17:32:16 2004 From: d.counsell at rfcgr.mrc.ac.uk (Damian Counsell) Date: Tue, 10 Feb 2004 17:32:16 +0000 Subject: the Matrix (reloaded) Message-ID: <20040210173216.GF26975@dev4.hgmp.mrc.ac.uk> EMBOSSnians! Did anyone get around to writing something to write scoring matrices (corresponding to the existing functions to read matrices)? ajMatrixRead --> ajMatrixWrite ajMatrixfRead --> ajMatrixfWrite all the best Damian -- MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SB, UK phone: +44 (0)1223 494585 fax: +44 (0)1223 494512 email: d.counsell at hgmp.mrc.ac.uk Web: http://www.rfcgr.mrc.ac.uk/~dcounsel/ From gbottu at ben.vub.ac.be Fri Feb 13 11:46:56 2004 From: gbottu at ben.vub.ac.be (Guy Bottu) Date: Fri, 13 Feb 2004 12:46:56 +0100 Subject: remarks about sequence formats Message-ID: <20040213114656.GA26101@bigben.ulb.ac.be> Dear developers, I just installed EMBOSS 2.8.0 at the BEN site. I did some testing and I noticed the following things about file formats : - the documentation says that "phylip" is non-interleaved format and "phylip3" interleaved format, but the programs write exactly the reverse ("phylip3::myseqs" has the sequences the one after the other and "phylip::myseqs" has them interleaved) - PAUP format is always written with "datatype=DNA", also when the sequences are proteins - an old pain in the ass : Staden "experiment" format is still not handled. I include an "experiment" file as attachment. As far as I know the differences with EMBL format are : - more field types - AC not mandatory - only 1 sequence per file - data fields allowed behind the sequence Note the AV lines with the "confidence values" of the bases. EMBOSS library routines to read and write these could be useful. There is software that can do something intelligent with "confidence values", e.g. Primer3, but at the present eprimer3 cannot handle them. Regards, Guy Bottu -------------- next part -------------- ID 000256_11cR EN 000256_11cR LN 000256_11cR..ztr LT ZTR AQ 50.180000 AV 18 20 18 18 19 13 13 6 6 6 6 6 9 7 8 11 11 21 24 32 39 46 40 AV 33 34 29 29 29 26 20 20 26 22 26 42 46 51 51 45 40 32 32 AV 32 33 34 32 24 17 13 10 10 19 19 28 28 28 29 35 35 40 39 AV 51 51 51 46 46 42 42 42 46 46 51 51 56 56 51 51 51 51 46 AV 40 35 35 35 39 39 39 56 51 51 51 51 39 39 39 39 39 39 45 AV 40 45 45 45 51 51 51 51 51 51 51 45 45 45 45 51 51 56 56 AV 51 51 51 51 51 51 56 56 56 56 56 56 56 56 56 56 56 51 51 AV 51 51 45 45 51 51 51 40 51 51 45 45 45 40 40 43 43 43 43 AV 45 51 45 56 51 51 51 51 51 45 45 45 45 45 45 51 51 51 51 AV 45 45 51 51 51 51 56 56 56 56 56 56 51 51 51 51 51 56 56 AV 56 51 51 51 51 51 51 56 56 56 56 56 56 56 56 46 43 43 43 AV 43 43 43 51 43 43 43 43 43 43 56 56 56 56 56 56 56 56 56 AV 56 56 51 45 45 45 45 45 51 51 51 51 51 56 56 51 56 56 51 AV 51 51 51 51 51 51 56 56 56 56 51 51 51 51 51 51 56 51 51 AV 51 51 51 51 56 56 56 56 56 51 51 51 51 51 51 51 51 56 56 AV 56 56 56 56 56 45 45 45 43 43 43 46 46 46 51 56 56 56 51 AV 51 51 56 56 45 45 45 45 45 45 56 56 56 56 56 56 56 56 56 AV 51 51 51 51 51 51 43 43 43 43 43 43 43 45 45 45 45 45 46 AV 43 43 43 43 43 43 51 56 43 43 43 43 43 43 51 51 46 46 46 AV 46 51 46 51 51 51 51 51 51 56 56 56 51 45 45 45 45 45 45 AV 51 51 51 56 51 51 51 51 51 51 51 56 56 56 56 56 56 51 51 AV 45 45 45 45 45 45 51 51 56 56 56 56 56 56 56 56 56 56 56 AV 56 51 51 51 45 45 45 45 45 45 43 43 43 43 43 43 43 43 43 AV 46 46 51 41 40 45 45 45 45 51 51 45 51 51 45 45 45 45 45 AV 45 45 45 45 45 45 45 45 45 51 56 56 56 56 56 56 56 56 56 AV 56 51 51 51 45 45 45 40 40 37 37 37 40 56 51 56 56 56 51 AV 51 51 51 51 51 56 45 45 45 45 40 40 45 45 40 40 45 45 40 AV 40 45 45 51 51 51 51 46 46 40 51 40 37 37 37 40 45 45 45 AV 45 56 45 40 35 35 35 32 32 35 46 42 51 51 51 46 46 37 35 AV 35 35 35 39 40 40 40 35 35 35 35 35 35 42 42 46 46 46 40 AV 40 40 40 40 38 42 42 27 19 11 11 11 28 27 40 40 40 44 32 AV 32 29 29 15 20 18 24 14 19 9 10 10 19 27 37 25 25 25 24 AV 29 29 29 20 12 12 13 12 15 12 11 8 8 8 8 7 7 7 4 0 0 0 AV 0 0 0 0 0 SQ GTGGGCAGAA AAGTTGACAT TCCTCTTCTG CATTTCCTGG ATTGAAAACA GAGCAAATGA CTGGCGCTTT GAAACCTTGA ATGTATTCTG CAAATACTGA GCATCAAGTT CACTTTCTTC CATTTCTATG CTTGTTTCCC GACTGTGGTT AACTTCATGT CCCAATGGAT ACTTAAAGCC TTCTGTGTCA TTTCTATTAT CTTTGGAACA ACCATGAATT AGTCCCTTGG GGTTTTCAAA TGCTGCACAC TGACTCACAC ATTTATTTGG TTCTGTTTTT GCCTTCCCTA GAGTGCTAAC TTCCAGTAAC GAGATACTTT CCTGAGTGCC ATAATCAGTA CCAGGTACCA GTGAAATACT GCTACTCTCT ACAGATCTTT CAGTTTGCAA AACCCTTTCT CCACTTAACA TGAGATCTTT GGGGTCTTCA GCATTATTAG ACACTTTAAC TGTTTCTAGT TTCTCTTCTT TTTCTTCTCT TGGAAGGCTA GGATTGACAA ATTCTTTAAG TTCACTGGTA TTTGAACACT TAGTAAAAGA ACCAGGTGCA TTTGTTAACT TCAGCTCTGG GAAAGTATCA CTGTCATGTC TTTTACTTGT CTGTTCATTT GGCACTGGCC GTCGCGCTTC ANNNNNNNN // TN 000256_11c PR 2 QL 17 QR 617 WT /home/gbottu/demo/exercise_snip/000906_11cR.scf WL -1 WR -1 TG MUTA - 50..50 TG C->T Sensitivity= 7.86, Alignment=0.14, Width=0.86, Amplitude=643 TG MUTA - 351..351 TG T->C Sensitivity= 8.13, Alignment=0.07, Width=1.00, Amplitude=1105 TG MUTA - 580..580 TG C->T Sensitivity= 6.19, Alignment=0.29, Width=1.21, Amplitude=1338 TG HETE - 585..585 TG AG Ratio=0.87, Alignment=0.00, Amplitude1=0.18, Amplitude2=0.15 From pmr at ebi.ac.uk Fri Feb 13 11:49:28 2004 From: pmr at ebi.ac.uk (Peter Rice) Date: Fri, 13 Feb 2004 11:49:28 +0000 Subject: remarks about sequence formats In-Reply-To: <20040213114656.GA26101@bigben.ulb.ac.be> References: <20040213114656.GA26101@bigben.ulb.ac.be> Message-ID: <402CB9C8.9050708@ebi.ac.uk> Guy Bottu wrote: > Dear developers, > > I just installed EMBOSS 2.8.0 at the BEN site. I did some testing and I > noticed the following things about file formats : Many thanks. There are also some problems with Nexus files for unaligned sequences, to be fixed in 2.8.1 regards, Peter From gbottu at ben.vub.ac.be Fri Feb 13 20:16:57 2004 From: gbottu at ben.vub.ac.be (Guy Bottu) Date: Fri, 13 Feb 2004 21:16:57 +0100 Subject: Staden and EMBOSS 2.8.O Message-ID: <20040213201657.GB29575@bigben.ulb.ac.be> Dear colleagues, As you all know, with EMBOSS 2.8.O the syntax of the ACD files has changed. An unfortunate consequence is that EMBOSS programs do not work well or not at all anymore under Staden spin or spin2. The script acd2tcl.tcl should be updated as to handle new things like the rename required -> standard and the use of $acdprotein. Unfortunately there is no support for Staden anymore (well, it was recently announced that James Bonfield is working at Sanger Centre, but according to the Web page he is only developing gap4, not spin). Does someone know more about it ? Guy Bottu, BEN From d.counsell at rfcgr.mrc.ac.uk Tue Feb 17 14:54:51 2004 From: d.counsell at rfcgr.mrc.ac.uk (Damian Counsell) Date: Tue, 17 Feb 2004 14:54:51 +0000 Subject: EMBOSS/Jemboss mentioned on Slashdot Message-ID: <20040217145451.GD1977@dev4.hgmp.mrc.ac.uk> EMBOSSnians! I am a pretty infrequent Slashdot reader these days so I've only just noticed that an article about BioKnoppix---featuring EMBOSS and Jemboss very prominently---appeared on /. this Saturday just gone: http://slashdot.org/article.pl?sid=04/02/14/188237 . In fact, it's so long since I visited there that I have moderator access. I feel one of my Alastair Campbell moments coming on. (If only some of the commenters were actually talking about the story itself so I could spin the debate in EMBOSS's favour properly.) all the best Damian -- MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SB, UK phone: +44 (0)1223 494585 fax: +44 (0)1223 494512 email: d.counsell at hgmp.mrc.ac.uk Web: http://www.rfcgr.mrc.ac.uk/~dcounsel/ From pmr at ebi.ac.uk Mon Feb 23 10:22:37 2004 From: pmr at ebi.ac.uk (Peter Rice) Date: Mon, 23 Feb 2004 10:22:37 +0000 Subject: [EMBOSS] Staden and EMBOSS 2.8.O In-Reply-To: <2DC41140A89ED411989D00508BDCD9ED01E28CD0@bi-exsrv1.iapc.bbsrc.ac.uk> References: <2DC41140A89ED411989D00508BDCD9ED01E28CD0@bi-exsrv1.iapc.bbsrc.ac.uk> Message-ID: <4039D46D.6000305@ebi.ac.uk> simon andrews (BI) wrote: > >>-----Original Message----- >>From: Guy Bottu [mailto:gbottu at ben.vub.ac.be] >>Subject: [EMBOSS] Staden and EMBOSS 2.8.O >> >>Unfortunately there is no support for Staden anymore (well, >>it was recently announced that James Bonfield is working >>at Sanger Centre, but according to the Web page he is >>only developing gap4, not spin). Does someone know more about it ? > > > James recently announced that the MRC have finally agreed to release Staden under an opensource licence. It is therefore now being hosted and developed as a sourceforge project: > > http://staden.sourceforge.net/ > > https://sourceforge.net/projects/staden > > ..therefore if you're up to making the changes yourself you can submit patches to the project, or if not you can file it as a bug which someone else will hopefully pick up. I have updated EMBSOS in the past to produce graphics in SPIN for some proggrams that did not do it "normally". I recently volunteered to update SPIN for EMBOSS 2.8.1 (due out soon) and will put the updates on the Staden SourceForge site and into the EMBOSS distribution. James Bonfield is here on campus so we can easily coordinate this. I may have a volunteer to test the SPIN/EMBOSS interface - but more would be welcome! regards, Peter Rice From pmr at ebi.ac.uk Mon Feb 23 10:37:51 2004 From: pmr at ebi.ac.uk (Peter Rice) Date: Mon, 23 Feb 2004 10:37:51 +0000 Subject: Staden and EMBOSS 2.8.O Message-ID: <4039D7FF.8000404@ebi.ac.uk> simon andrews (BI) wrote: > >>-----Original Message----- >>From: Guy Bottu [mailto:gbottu at ben.vub.ac.be] >>Subject: [EMBOSS] Staden and EMBOSS 2.8.O >> >>Unfortunately there is no support for Staden anymore (well, >>it was recently announced that James Bonfield is working >>at Sanger Centre, but according to the Web page he is >>only developing gap4, not spin). Does someone know more about it ? > > > James recently announced that the MRC have finally agreed to release Staden under an opensource licence. It is therefore now being hosted and developed as a sourceforge project: > > http://staden.sourceforge.net/ > > https://sourceforge.net/projects/staden > > ..therefore if you're up to making the changes yourself you can submit patches to the project, or if not you can file it as a bug which someone else will hopefully pick up. I have updated EMBOSS in the past to produce graphics in SPIN for some programs that did not do it "normally". I recently volunteered to update SPIN for EMBOSS 2.8.1 (due out soon) and will put the updates on the Staden SourceForge site and into the EMBOSS distribution. James Bonfield is here on campus so we can easily coordinate this. I may have a volunteer to test the SPIN/EMBOSS interface - but more would be welcome! regards, Peter Rice From gbottu at ben.vub.ac.be Thu Feb 26 11:04:16 2004 From: gbottu at ben.vub.ac.be (Guy Bottu) Date: Thu, 26 Feb 2004 12:04:16 +0100 Subject: The empty file problem Message-ID: <20040226110416.GA29428@bigben.ulb.ac.be> from : BEN Dear developers, Can I point your attention to a (minor) problem ? When you run e.g. the program charge on sw:papa_carpa it creates a file papa_carpa.charge. If you run it with parameter -plot it will create a graphic but it will also create an empty file papa_carpa.charge. If a papa_carpa.charge from a previous run existed already it is overwritten. Wouldn't it be appropriate to add to : outfile: outfile [ standard: "@(!$(plot))" knowntype: "charge output" ] a line : nullok: "$(plot)" The same problem also exists for dan, findk, freak, hmoment, iep, syco and tcode. Regards, Guy Bottu