From gwilliam at hgmp.mrc.ac.uk Tue Apr 23 05:07:23 2002 From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522) Date: Tue, 23 Apr 2002 10:07:23 +0100 Subject: [Fwd: Tranalign] Message-ID: <3CC5244B.4DCA4027@hgmp.mrc.ac.uk> Is another release due soon? Gary Georgia Panopoul wrote: > > Dear Dr. Williams, > > I am interested in using the tranalign program that you have included in > the emboss package. However, the current release of emboss (EMBOSS-2.3.1) > does not include the tranalign although in the main page of emboss > (http://www.emboss.org/) describing the applications included, it is > listed as included. > > Please let me know whether there is any possibility to download the > tranalign programme separate from emboss. > > Sincerely, > Georgia Panopoulou > > ---------------------------------------------------------------------------- > Georgia Panopoulou, PhD > Max-Planck Institute for Molekular Genetics > Evolution and Development Group > Abt. Lehrach > Ihnestrasse 73 Tel: +49-30-84131235 > D-14195 Berlin Fax: +49-30-84131380 > Germany email: panopoul at molgen.mpg.de > ----------------------------------------------------------------------------- -- Gary Williams Tel: +44 1223 494522 Fax: +44 1223 494512 mailto:G.Williams at hgmp.mrc.ac.uk http://www.hgmp.mrc.ac.uk/ Bioinformatics,MRC HGMP Resource Centre,Hinxton,Cambridge, CB10 1SB,UK From peter.rice at uk.lionbioscience.com Tue Apr 23 05:11:50 2002 From: peter.rice at uk.lionbioscience.com (Peter Rice) Date: Tue, 23 Apr 2002 10:11:50 +0100 Subject: [Fwd: Tranalign] References: <3CC5244B.4DCA4027@hgmp.mrc.ac.uk> Message-ID: <3CC52556.9A231509@uk.lionbioscience.com> "Gary Williams, Tel 01223 494522" wrote: > > Is another release due soon? > Gary Yes, once the USA query extensions are completed. The ChangeLog file gets ever longer. I expect we can discuss this at the next EMBOSS meeting (in 2 weeks time.) But ... did you mean to mail the question to emboss-dev ??? Peter -- ------------------------------------------------ Peter Rice, LION Bioscience Ltd, Cambridge, UK peter.rice at uk.lionbioscience.com +44 1223 224723 From peter.rice at uk.lionbioscience.com Wed Apr 24 05:37:09 2002 From: peter.rice at uk.lionbioscience.com (Peter Rice) Date: Wed, 24 Apr 2002 10:37:09 +0100 Subject: Pise/EMBOSS 2.3.1 References: Message-ID: <3CC67CC5.85EAB7C3@uk.lionbioscience.com> David Mathog wrote: > > Back to the subject at hand. (And this is stream of consciousness, so > please > bear with me.) I think that maybe for purposes of interface design there > should be predefined methods to break out (all) the pieces/options of a > USA. Discussion transferred to emboss-dev ... For filename USAs there are already associated qualifiers for most parts. It looks to me as though you are really asking for associated qualifiers for all the bits of USAs. If these qualifiers can also appear in listfiles then they will work there too. GUIs are then free to display whatever they want, and to pass the bits to EMBOSS to reassemble. All the qualifiers should start with -s (like -sformat) to keep them consistent. For USAs like genbank:* it gets a little tricky ... that is an EMBOSS database definition, but maybe the bits of a database definition could be passed in the USA too (look at emboss.default to see what you would need). We could allow incomplete database definitions for that, for example by adding a new database attribute (so showdb can warn about them), or the command line could override settings in emboss.default. How the GUI handles all this is of course not an EMBOSS problem :-) I assume no GUI will want to use all the USA options, but they can make life easier. GUI developers ... what extra USA associated qualifiers would you like? Peter -- ------------------------------------------------ Peter Rice, LION Bioscience Ltd, Cambridge, UK peter.rice at uk.lionbioscience.com +44 1223 224723 From jkb at mrc-lmb.cam.ac.uk Wed Apr 24 05:46:23 2002 From: jkb at mrc-lmb.cam.ac.uk (James Bonfield) Date: Wed, 24 Apr 2002 10:46:23 +0100 Subject: Pise/EMBOSS 2.3.1 In-Reply-To: <3CC67CC5.85EAB7C3@uk.lionbioscience.com>; from peter.rice@uk.lionbioscience.com on Wed, Apr 24, 2002 at 10:37:09AM +0100 References: <3CC67CC5.85EAB7C3@uk.lionbioscience.com> Message-ID: <20020424104623.B25968@arran.mrc-lmb.cam.ac.uk> On Wed, Apr 24, 2002 at 10:37:09AM +0100, Peter Rice wrote: > GUI developers ... what extra USA associated qualifiers would you like? In Spin things are a little bit different than expected. Spin has a 2-stage affair where sequences are firstly loaded into memory (either by direct file access or remote access via emboss). From here sequences are manipulated internally or new sequences can be created (ie rotations, translations, scrambling, etc). It is the in-memory sequences which are then passed to EMBOSS. Currently this is done by writing them out to a temporary file in a known format (EMBL including with feature tables). We have the option to chose a start and end point, but they're the only options. Hence most of the USA parts of EMBOSS are not needed by us except perhaps for the initial File->Load option. James -- James Bonfield (jkb at mrc-lmb.cam.ac.uk) Fax: (+44) 01223 213556 Medical Research Council - Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 2QH, England. Also see Staden Package WWW site at http://www.mrc-lmb.cam.ac.uk/pubseq/ From gwilliam at hgmp.mrc.ac.uk Tue Apr 23 09:07:23 2002 From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522) Date: Tue, 23 Apr 2002 10:07:23 +0100 Subject: [Fwd: Tranalign] Message-ID: <3CC5244B.4DCA4027@hgmp.mrc.ac.uk> Is another release due soon? Gary Georgia Panopoul wrote: > > Dear Dr. Williams, > > I am interested in using the tranalign program that you have included in > the emboss package. However, the current release of emboss (EMBOSS-2.3.1) > does not include the tranalign although in the main page of emboss > (http://www.emboss.org/) describing the applications included, it is > listed as included. > > Please let me know whether there is any possibility to download the > tranalign programme separate from emboss. > > Sincerely, > Georgia Panopoulou > > ---------------------------------------------------------------------------- > Georgia Panopoulou, PhD > Max-Planck Institute for Molekular Genetics > Evolution and Development Group > Abt. Lehrach > Ihnestrasse 73 Tel: +49-30-84131235 > D-14195 Berlin Fax: +49-30-84131380 > Germany email: panopoul at molgen.mpg.de > ----------------------------------------------------------------------------- -- Gary Williams Tel: +44 1223 494522 Fax: +44 1223 494512 mailto:G.Williams at hgmp.mrc.ac.uk http://www.hgmp.mrc.ac.uk/ Bioinformatics,MRC HGMP Resource Centre,Hinxton,Cambridge, CB10 1SB,UK From peter.rice at uk.lionbioscience.com Tue Apr 23 09:11:50 2002 From: peter.rice at uk.lionbioscience.com (Peter Rice) Date: Tue, 23 Apr 2002 10:11:50 +0100 Subject: [Fwd: Tranalign] References: <3CC5244B.4DCA4027@hgmp.mrc.ac.uk> Message-ID: <3CC52556.9A231509@uk.lionbioscience.com> "Gary Williams, Tel 01223 494522" wrote: > > Is another release due soon? > Gary Yes, once the USA query extensions are completed. The ChangeLog file gets ever longer. I expect we can discuss this at the next EMBOSS meeting (in 2 weeks time.) But ... did you mean to mail the question to emboss-dev ??? Peter -- ------------------------------------------------ Peter Rice, LION Bioscience Ltd, Cambridge, UK peter.rice at uk.lionbioscience.com +44 1223 224723 From peter.rice at uk.lionbioscience.com Wed Apr 24 09:37:09 2002 From: peter.rice at uk.lionbioscience.com (Peter Rice) Date: Wed, 24 Apr 2002 10:37:09 +0100 Subject: Pise/EMBOSS 2.3.1 References: Message-ID: <3CC67CC5.85EAB7C3@uk.lionbioscience.com> David Mathog wrote: > > Back to the subject at hand. (And this is stream of consciousness, so > please > bear with me.) I think that maybe for purposes of interface design there > should be predefined methods to break out (all) the pieces/options of a > USA. Discussion transferred to emboss-dev ... For filename USAs there are already associated qualifiers for most parts. It looks to me as though you are really asking for associated qualifiers for all the bits of USAs. If these qualifiers can also appear in listfiles then they will work there too. GUIs are then free to display whatever they want, and to pass the bits to EMBOSS to reassemble. All the qualifiers should start with -s (like -sformat) to keep them consistent. For USAs like genbank:* it gets a little tricky ... that is an EMBOSS database definition, but maybe the bits of a database definition could be passed in the USA too (look at emboss.default to see what you would need). We could allow incomplete database definitions for that, for example by adding a new database attribute (so showdb can warn about them), or the command line could override settings in emboss.default. How the GUI handles all this is of course not an EMBOSS problem :-) I assume no GUI will want to use all the USA options, but they can make life easier. GUI developers ... what extra USA associated qualifiers would you like? Peter -- ------------------------------------------------ Peter Rice, LION Bioscience Ltd, Cambridge, UK peter.rice at uk.lionbioscience.com +44 1223 224723 From jkb at mrc-lmb.cam.ac.uk Wed Apr 24 09:46:23 2002 From: jkb at mrc-lmb.cam.ac.uk (James Bonfield) Date: Wed, 24 Apr 2002 10:46:23 +0100 Subject: Pise/EMBOSS 2.3.1 In-Reply-To: <3CC67CC5.85EAB7C3@uk.lionbioscience.com>; from peter.rice@uk.lionbioscience.com on Wed, Apr 24, 2002 at 10:37:09AM +0100 References: <3CC67CC5.85EAB7C3@uk.lionbioscience.com> Message-ID: <20020424104623.B25968@arran.mrc-lmb.cam.ac.uk> On Wed, Apr 24, 2002 at 10:37:09AM +0100, Peter Rice wrote: > GUI developers ... what extra USA associated qualifiers would you like? In Spin things are a little bit different than expected. Spin has a 2-stage affair where sequences are firstly loaded into memory (either by direct file access or remote access via emboss). From here sequences are manipulated internally or new sequences can be created (ie rotations, translations, scrambling, etc). It is the in-memory sequences which are then passed to EMBOSS. Currently this is done by writing them out to a temporary file in a known format (EMBL including with feature tables). We have the option to chose a start and end point, but they're the only options. Hence most of the USA parts of EMBOSS are not needed by us except perhaps for the initial File->Load option. James -- James Bonfield (jkb at mrc-lmb.cam.ac.uk) Fax: (+44) 01223 213556 Medical Research Council - Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 2QH, England. Also see Staden Package WWW site at http://www.mrc-lmb.cam.ac.uk/pubseq/