From ableasby at hgmp.mrc.ac.uk Wed Oct 4 12:05:59 2000 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Wed, 4 Oct 2000 17:05:59 +0100 (BST) Subject: emboss 1.5.6 Message-ID: <200010041605.RAA11085@tin.hgmp.mrc.ac.uk> >From the perspective of using EMBOSS this release allows URL access to SRS 6.0.7.* servers (LION changed the result format for their latest version), it also corrects some GenBank problems. >From a nuts and bolts perspective the library is now, to my knowledge, free of any memory leaks however minor. So are 98% of the applications ... the remaining 2% only leak a few bytes and will be spring-cleaned shortly. Alan From stein at fieldmuseum.org Wed Oct 4 12:46:12 2000 From: stein at fieldmuseum.org (Jennifer Steinbachs) Date: Wed, 4 Oct 2000 11:46:12 -0500 (CDT) Subject: AJAX fixed root? In-Reply-To: <200010041605.RAA11085@tin.hgmp.mrc.ac.uk> Message-ID: I'm just curious why AJAX fixed root is not, by default, set to ${prefix}. I don't tend to compile in the directory where I ultimately store the emboss (or any other) package. So, I have to go in manually and change AJAX_FIXED_ROOT for every makefile. Is there a way to specify this on the configure line? -jennifer ----------------------------------- J. Steinbachs, Ph.D. Computational Biologist The Field Museum Chicago, IL 60605-2496 office: 312-665-7810 fax: 312-665-7158 http://cb.fmnh.org ----------------------------------- From ableasby at hgmp.mrc.ac.uk Wed Oct 4 16:40:29 2000 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Wed, 4 Oct 2000 21:40:29 +0100 (BST) Subject: EMBOSS 1.5.6 addendum Message-ID: <200010042040.VAA11926@tin.hgmp.mrc.ac.uk> On the main server you'll find a patchfiles directory. This contains files that the current version of EMBOSS has been patched with since its first announcement. 1.5.6 has already been patched but only with a minor bugfix i.e. the "embossdata" program wasn't looking in the "make install" directory structure for the datafiles. So, you can either re-ftp 1.5.6 or just ftp any patchfiles and re-make. You will also find a file called "embossre.equ" in that directory. This is an update from Helge Horch. It is the EMBOSS datafile that modifies the action of "restrict" if the -preferred option is given i.e. names of more commonly available equivalent cutters are shown rather than the first alphabetical cutter. Alan From tcarver at hgmp.mrc.ac.uk Fri Oct 6 10:45:15 2000 From: tcarver at hgmp.mrc.ac.uk (Tim Carver) Date: Fri, 06 Oct 2000 15:45:15 +0100 Subject: EMBOSS 1.6.0 Message-ID: <39DDE57A.CE4ECE8A@hgmp.mrc.ac.uk> EMBOSS 1.6.0 has now been released. Two new applications: (1) cons - calculates a consensus sequence from a multiple sequence alignment. To obtain the consensus, the sequence weights and a scoring matrix are used to calculate a score at each position in the alignment. The "plurality" option allows the user to set a cut-off for the number of positive matches below which there is no consensus. The "identity" option provides the facility of setting the required number of identities at a site for it to give a consensus at that position. Therefore, if this is set to the number of sequences in the alignment only columns of identities contribute to the consensus. The "setcase" option sets the threshold for the positive matches above which the consensus is is upper-case and below which the consensus is in lower-case. (2) plotcon - displays a graphical representation of the similarity along a set of aligned sequences. The similarity is calculated by moving a window of a specified length along the aligned sequences. Within the window, the similarity of any one position is taken to be the average of all the possible pairwise scores of the bases or residues at that position. The pairwise scores are taken from the specified similarity matrix. The average of the position similarities within the window is plotted. The program may be useful is determining where the quality of alignments are good or bad. Tim -- Tim Carver, PhD, Bioinformatics, MRC HGMP Resource Centre, Hinxton, Cambridge, CB10 1SB -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.open-bio.org/pipermail/emboss/attachments/20001006/c3be9d1e/attachment.html From johann at egenetics.com Mon Oct 9 06:56:58 2000 From: johann at egenetics.com (Johann Visagie) Date: Mon, 9 Oct 2000 12:56:58 +0200 Subject: FreeBSD EMBOSS port updated Message-ID: <20001009125658.A34039@fling.sanbi.ac.za> I've just submitted a PR to update the FreeBSD port of EMBOSS from 1.5.0 to 1.6.0. I've been a bit swamped lately, and have been unable to keep the porting up to date with all the EMBOSS 1.5 point releases. http://www.freebsd.org/cgi/query-pr.cgi?pr=21857 -- Johann From ableasby at hgmp.mrc.ac.uk Wed Oct 11 13:57:13 2000 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Wed, 11 Oct 2000 18:57:13 +0100 (BST) Subject: EMBOSS 1.6.1 Message-ID: <200010111757.SAA23092@tin.hgmp.mrc.ac.uk> Had to put this one out as the latest release of RedHat (7.0, just released) has messed about with its header files (fpos_t) causing compilation failure. Alan From ableasby at hgmp.mrc.ac.uk Mon Oct 23 11:34:19 2000 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Mon, 23 Oct 2000 16:34:19 +0100 (BST) Subject: EMBOSS 1.6.2 Message-ID: <200010231534.QAA22758@tin.hgmp.mrc.ac.uk> Amongst numerous minor changes this adds the ability to read SEQED-mangled gcg files. It also fixes some problems in PHYLIP output. The CODCMP application has been modified by David Martin. Alan From ableasby at hgmp.mrc.ac.uk Tue Oct 24 19:23:59 2000 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Wed, 25 Oct 2000 00:23:59 +0100 (BST) Subject: EMBOSS 1.6.3 Message-ID: <200010242323.AAA28698@tin.hgmp.mrc.ac.uk> This includes a rewrite of the profile library routines. PROPHET should not be so fragile now. Bowing to demand I've added some percent ID and percent similarity statistics to NEEDLE and WATER. You can turn it off if its a nuisance. Some sort of 'expect' statistic will be added later. I've also added a fasta output option to the latter programs. The mangling of GCG files by SEQED turned out to have an inconsistent format. This release should cope with such cases that have been reported. Alan From johann at egenetics.com Tue Oct 31 07:19:01 2000 From: johann at egenetics.com (Johann Visagie) Date: Tue, 31 Oct 2000 14:19:01 +0200 Subject: Any EMBOSS releases planned? Message-ID: <20001031141901.D815@fling.sanbi.ac.za> Any new EMBOSS point-releases planned for the next few days? FreeBSD is entering ports freeze at 19:00 GMT on Friday the 3rd in preparation for the 4.2 release of the OS, and I would like to get the "latest, greatest" EMBOSS to go out on those distribution CDs. :-) If no new releases are planned, I'll just update the port to 1.6.3 now. -- Johann From david.martin at biotek.uio.no Tue Oct 31 07:49:20 2000 From: david.martin at biotek.uio.no (David Martin) Date: Tue, 31 Oct 2000 12:49:20 +0000 Subject: To do list. Message-ID: Having just seen the 'to do' list on the web can I throw my spanner in.. Could the results output from a number of programs be modified in the following way: A results object (in much the same way as a sequence object) is created. The program author doesn't have to worry about any formatting because the result object knows about it. New output styles get added at a library level, not an application level. This sprang out of looking at the code for INFOSEQ with the thought of having output into an SQL database. As every statement seems to have if (html) else it looked somewhat ugly. Having consistent result objects would be very nice for downstream parsers and integration into all sorts of other things. I know I am guilty of having a hideous output format in the apps I have written but am more than prepared to rewrite them. It also means that we can get programs written easier, better code output from the various formats (eg tagging each HTML tag with class=emboss-result etc so local style sheets can be used), XML for integration with Kathrine and Kates various interfaces and so on. Suggested initial result types: 1) Single value lists: These are lists of single values for example the output from infoseq, geecee, btwisted. Labelled with sequence ID and then a list of results. 2.) Composition tables (eg cusp, compseq and so on) 3.) Site lists as feature tables? eg restrict. Add to this every program that puts out output having a standard format header to say which program, when, where, and giving the parameters. In addition to this, a new database access format. Not sequences but codon usage. The codon usage tables distributed with emboss are positively fossilised (6 years old). An access method for reading a species from CUTG .spsum files would be great. Extracting all species from CUTG is probably a bit over the top so an access method for just the interesting species should suffice. Showdb should then show a C as the database type. ..d --------------------------------------------------------------------- * Dr. David Martin Biotechnology Centre of Oslo * * Node Manager Gaustadalleen 21 * * The Norwegian EMBNet Node P.O. box 1125 Blindern * * tel +47 22 84 05 35 N-0317 Oslo * * fax +47 22 84 05 01 Norway * --------------------------------------------------------------------- From Peter.Rice at uk.lionbioscience.com Tue Oct 31 08:14:50 2000 From: Peter.Rice at uk.lionbioscience.com (Peter Rice) Date: Tue, 31 Oct 2000 13:14:50 +0000 Subject: To do list. References: Message-ID: <39FEC5CA.E44CCD18@lionbio.co.uk> David Martin wrote: > Having just seen the 'to do' list on the web can I throw my spanner in.. > > Could the results output from a number of programs be modified in the > following way: > > A results object (in much the same way as a sequence object) is > created. The program author doesn't have to worry about any formatting > because the result object knows about it. > New output styles get added at a library level, not an application level. This is top of my list of things to do. My initial plan is to add a new output type of 'report' which will use data stored internally as a feature table and will generate various output formats. These will include the existing feature formats (e.g. GFF and EMBL) but also include formats rather similar to the results of 'restrict' 'antigenic' and other programs that effectively report 'features'. The applications will need (often minor) changes to store results in a feature table. This works too for simple lists and the other output types you mentioned. Default 'formats' can be included in the ACD file. An output type and a format combination would work nicely (with the output type saying what the program will pass, and the format available on the command line as an associated qualifier). New formats can be easily added (like sequence formats) by extending the report generating code. >In addition to this, a new database access format. Not sequences but codon >usage. The codon usage tables distributed with emboss are positively >fossilised (6 years old). An access method for reading a species from CUTG >.spsum files would be great. Something like an SRS query (possibly through a remote SRS web server) perhaps? Something could be defined as a database in emboss.defaults and used by the codon usage table code. It would create the need for a new standard for naming codon usage tables, and a new name for it. Maybe ACA (A CUT above?) Or you could just ask for the code and then look in (1) a codon usage file and (2) some standard database name -- ------------------------------------------------ Peter Rice, LION Bioscience Ltd, Cambridge, UK peter.rice at uk.lionbioscience.com +44 1223 224723 From johann at egenetics.com Tue Oct 31 08:46:58 2000 From: johann at egenetics.com (Johann Visagie) Date: Tue, 31 Oct 2000 15:46:58 +0200 Subject: EMBOSS/Exceed solution In-Reply-To: <200008020933.KAA10553@bromine.hgmp.mrc.ac.uk>; from ableasby@hgmp.mrc.ac.uk on Wed, Aug 02, 2000 at 10:33:02AM +0100 References: <200008020933.KAA10553@bromine.hgmp.mrc.ac.uk> Message-ID: <20001031154658.M815@fling.sanbi.ac.za> ableasby at hgmp.mrc.ac.uk on 2000-08-02 (Wed) at 10:33:02 +0100: > > Well, it works for us anyway. Val and I have had a look on two > exceed setups, one where it failed and one where it worked. > As we suspected it was a trucolor problem where the failure > occurred. > > Go to the exceed configuration. Click on Screen Definition, then > set Server Visual to Pseudocolour and hopefully it'll work. It seems that this problem is not specific to Exceed. A user here recently encountered an identical problem using X-Win 32 (another X Server for Windows). The solution was identical (though I can't recall exactly where in the X-Win 32 configuration screens the change had to be made). -- Johann From ableasby at hgmp.mrc.ac.uk Tue Oct 31 11:35:05 2000 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Tue, 31 Oct 2000 16:35:05 GMT Subject: EMBOSS 1.7.0 Message-ID: <200010311635.QAA12918@tin.hgmp.mrc.ac.uk> NB: The default operation of -osf gcg has changed with 1.7.0 The same applies to the staden, plain, text & experiment formats. The problem with all the above formats is that if you retrieved multiple sequences they would all go into the same file. This would, of course, be meaningless. The strange thing is that that's precisely what we've decided to do in this release. Old behaviour for (e.g.) -osf gcg: The output filename would be ignored and EMBOSS would generate filenames automatically. This was confusing a lot of people.... especially as it wasn't really documented. To get it to have the same behaviour as all the other formats the switch -noossingle had to be used. New behaviour: It now recognises the output filename. This means that it is up to you to make sure you only retrieve single sequences. If you want to retrieve multiple sequences in GCG format you must send them to single files by putting -ossingle on the command line. At least the behaviour is now consistent and, if you're feeling perverse, you could use this feature for catenating sequences in plain format instead of pasteseq! ENTRET: This application is a bit like SEQRET but retrieves whole database entries in their original format. It works only with flatfiles (e.g. indexed by dbiflat) and is currently only implemented for EMBL & GenBank format databases. A long-standing problem of -slower and -supper only converting the first sequence in multi-sequence retrieval has been fixed. Alan From ableasby at hgmp.mrc.ac.uk Wed Oct 4 16:05:59 2000 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Wed, 4 Oct 2000 17:05:59 +0100 (BST) Subject: emboss 1.5.6 Message-ID: <200010041605.RAA11085@tin.hgmp.mrc.ac.uk> >From the perspective of using EMBOSS this release allows URL access to SRS 6.0.7.* servers (LION changed the result format for their latest version), it also corrects some GenBank problems. >From a nuts and bolts perspective the library is now, to my knowledge, free of any memory leaks however minor. So are 98% of the applications ... the remaining 2% only leak a few bytes and will be spring-cleaned shortly. Alan From stein at fieldmuseum.org Wed Oct 4 16:46:12 2000 From: stein at fieldmuseum.org (Jennifer Steinbachs) Date: Wed, 4 Oct 2000 11:46:12 -0500 (CDT) Subject: AJAX fixed root? In-Reply-To: <200010041605.RAA11085@tin.hgmp.mrc.ac.uk> Message-ID: I'm just curious why AJAX fixed root is not, by default, set to ${prefix}. I don't tend to compile in the directory where I ultimately store the emboss (or any other) package. So, I have to go in manually and change AJAX_FIXED_ROOT for every makefile. Is there a way to specify this on the configure line? -jennifer ----------------------------------- J. Steinbachs, Ph.D. Computational Biologist The Field Museum Chicago, IL 60605-2496 office: 312-665-7810 fax: 312-665-7158 http://cb.fmnh.org ----------------------------------- From ableasby at hgmp.mrc.ac.uk Wed Oct 4 20:40:29 2000 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Wed, 4 Oct 2000 21:40:29 +0100 (BST) Subject: EMBOSS 1.5.6 addendum Message-ID: <200010042040.VAA11926@tin.hgmp.mrc.ac.uk> On the main server you'll find a patchfiles directory. This contains files that the current version of EMBOSS has been patched with since its first announcement. 1.5.6 has already been patched but only with a minor bugfix i.e. the "embossdata" program wasn't looking in the "make install" directory structure for the datafiles. So, you can either re-ftp 1.5.6 or just ftp any patchfiles and re-make. You will also find a file called "embossre.equ" in that directory. This is an update from Helge Horch. It is the EMBOSS datafile that modifies the action of "restrict" if the -preferred option is given i.e. names of more commonly available equivalent cutters are shown rather than the first alphabetical cutter. Alan From tcarver at hgmp.mrc.ac.uk Fri Oct 6 14:45:15 2000 From: tcarver at hgmp.mrc.ac.uk (Tim Carver) Date: Fri, 06 Oct 2000 15:45:15 +0100 Subject: EMBOSS 1.6.0 Message-ID: <39DDE57A.CE4ECE8A@hgmp.mrc.ac.uk> EMBOSS 1.6.0 has now been released. Two new applications: (1) cons - calculates a consensus sequence from a multiple sequence alignment. To obtain the consensus, the sequence weights and a scoring matrix are used to calculate a score at each position in the alignment. The "plurality" option allows the user to set a cut-off for the number of positive matches below which there is no consensus. The "identity" option provides the facility of setting the required number of identities at a site for it to give a consensus at that position. Therefore, if this is set to the number of sequences in the alignment only columns of identities contribute to the consensus. The "setcase" option sets the threshold for the positive matches above which the consensus is is upper-case and below which the consensus is in lower-case. (2) plotcon - displays a graphical representation of the similarity along a set of aligned sequences. The similarity is calculated by moving a window of a specified length along the aligned sequences. Within the window, the similarity of any one position is taken to be the average of all the possible pairwise scores of the bases or residues at that position. The pairwise scores are taken from the specified similarity matrix. The average of the position similarities within the window is plotted. The program may be useful is determining where the quality of alignments are good or bad. Tim -- Tim Carver, PhD, Bioinformatics, MRC HGMP Resource Centre, Hinxton, Cambridge, CB10 1SB -------------- next part -------------- An HTML attachment was scrubbed... URL: From johann at egenetics.com Mon Oct 9 10:56:58 2000 From: johann at egenetics.com (Johann Visagie) Date: Mon, 9 Oct 2000 12:56:58 +0200 Subject: FreeBSD EMBOSS port updated Message-ID: <20001009125658.A34039@fling.sanbi.ac.za> I've just submitted a PR to update the FreeBSD port of EMBOSS from 1.5.0 to 1.6.0. I've been a bit swamped lately, and have been unable to keep the porting up to date with all the EMBOSS 1.5 point releases. http://www.freebsd.org/cgi/query-pr.cgi?pr=21857 -- Johann From ableasby at hgmp.mrc.ac.uk Wed Oct 11 17:57:13 2000 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Wed, 11 Oct 2000 18:57:13 +0100 (BST) Subject: EMBOSS 1.6.1 Message-ID: <200010111757.SAA23092@tin.hgmp.mrc.ac.uk> Had to put this one out as the latest release of RedHat (7.0, just released) has messed about with its header files (fpos_t) causing compilation failure. Alan From ableasby at hgmp.mrc.ac.uk Mon Oct 23 15:34:19 2000 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Mon, 23 Oct 2000 16:34:19 +0100 (BST) Subject: EMBOSS 1.6.2 Message-ID: <200010231534.QAA22758@tin.hgmp.mrc.ac.uk> Amongst numerous minor changes this adds the ability to read SEQED-mangled gcg files. It also fixes some problems in PHYLIP output. The CODCMP application has been modified by David Martin. Alan From ableasby at hgmp.mrc.ac.uk Tue Oct 24 23:23:59 2000 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Wed, 25 Oct 2000 00:23:59 +0100 (BST) Subject: EMBOSS 1.6.3 Message-ID: <200010242323.AAA28698@tin.hgmp.mrc.ac.uk> This includes a rewrite of the profile library routines. PROPHET should not be so fragile now. Bowing to demand I've added some percent ID and percent similarity statistics to NEEDLE and WATER. You can turn it off if its a nuisance. Some sort of 'expect' statistic will be added later. I've also added a fasta output option to the latter programs. The mangling of GCG files by SEQED turned out to have an inconsistent format. This release should cope with such cases that have been reported. Alan From johann at egenetics.com Tue Oct 31 12:19:01 2000 From: johann at egenetics.com (Johann Visagie) Date: Tue, 31 Oct 2000 14:19:01 +0200 Subject: Any EMBOSS releases planned? Message-ID: <20001031141901.D815@fling.sanbi.ac.za> Any new EMBOSS point-releases planned for the next few days? FreeBSD is entering ports freeze at 19:00 GMT on Friday the 3rd in preparation for the 4.2 release of the OS, and I would like to get the "latest, greatest" EMBOSS to go out on those distribution CDs. :-) If no new releases are planned, I'll just update the port to 1.6.3 now. -- Johann From david.martin at biotek.uio.no Tue Oct 31 12:49:20 2000 From: david.martin at biotek.uio.no (David Martin) Date: Tue, 31 Oct 2000 12:49:20 +0000 Subject: To do list. Message-ID: Having just seen the 'to do' list on the web can I throw my spanner in.. Could the results output from a number of programs be modified in the following way: A results object (in much the same way as a sequence object) is created. The program author doesn't have to worry about any formatting because the result object knows about it. New output styles get added at a library level, not an application level. This sprang out of looking at the code for INFOSEQ with the thought of having output into an SQL database. As every statement seems to have if (html) else it looked somewhat ugly. Having consistent result objects would be very nice for downstream parsers and integration into all sorts of other things. I know I am guilty of having a hideous output format in the apps I have written but am more than prepared to rewrite them. It also means that we can get programs written easier, better code output from the various formats (eg tagging each HTML tag with class=emboss-result etc so local style sheets can be used), XML for integration with Kathrine and Kates various interfaces and so on. Suggested initial result types: 1) Single value lists: These are lists of single values for example the output from infoseq, geecee, btwisted. Labelled with sequence ID and then a list of results. 2.) Composition tables (eg cusp, compseq and so on) 3.) Site lists as feature tables? eg restrict. Add to this every program that puts out output having a standard format header to say which program, when, where, and giving the parameters. In addition to this, a new database access format. Not sequences but codon usage. The codon usage tables distributed with emboss are positively fossilised (6 years old). An access method for reading a species from CUTG .spsum files would be great. Extracting all species from CUTG is probably a bit over the top so an access method for just the interesting species should suffice. Showdb should then show a C as the database type. ..d --------------------------------------------------------------------- * Dr. David Martin Biotechnology Centre of Oslo * * Node Manager Gaustadalleen 21 * * The Norwegian EMBNet Node P.O. box 1125 Blindern * * tel +47 22 84 05 35 N-0317 Oslo * * fax +47 22 84 05 01 Norway * --------------------------------------------------------------------- From Peter.Rice at uk.lionbioscience.com Tue Oct 31 13:14:50 2000 From: Peter.Rice at uk.lionbioscience.com (Peter Rice) Date: Tue, 31 Oct 2000 13:14:50 +0000 Subject: To do list. References: Message-ID: <39FEC5CA.E44CCD18@lionbio.co.uk> David Martin wrote: > Having just seen the 'to do' list on the web can I throw my spanner in.. > > Could the results output from a number of programs be modified in the > following way: > > A results object (in much the same way as a sequence object) is > created. The program author doesn't have to worry about any formatting > because the result object knows about it. > New output styles get added at a library level, not an application level. This is top of my list of things to do. My initial plan is to add a new output type of 'report' which will use data stored internally as a feature table and will generate various output formats. These will include the existing feature formats (e.g. GFF and EMBL) but also include formats rather similar to the results of 'restrict' 'antigenic' and other programs that effectively report 'features'. The applications will need (often minor) changes to store results in a feature table. This works too for simple lists and the other output types you mentioned. Default 'formats' can be included in the ACD file. An output type and a format combination would work nicely (with the output type saying what the program will pass, and the format available on the command line as an associated qualifier). New formats can be easily added (like sequence formats) by extending the report generating code. >In addition to this, a new database access format. Not sequences but codon >usage. The codon usage tables distributed with emboss are positively >fossilised (6 years old). An access method for reading a species from CUTG >.spsum files would be great. Something like an SRS query (possibly through a remote SRS web server) perhaps? Something could be defined as a database in emboss.defaults and used by the codon usage table code. It would create the need for a new standard for naming codon usage tables, and a new name for it. Maybe ACA (A CUT above?) Or you could just ask for the code and then look in (1) a codon usage file and (2) some standard database name -- ------------------------------------------------ Peter Rice, LION Bioscience Ltd, Cambridge, UK peter.rice at uk.lionbioscience.com +44 1223 224723 From johann at egenetics.com Tue Oct 31 13:46:58 2000 From: johann at egenetics.com (Johann Visagie) Date: Tue, 31 Oct 2000 15:46:58 +0200 Subject: EMBOSS/Exceed solution In-Reply-To: <200008020933.KAA10553@bromine.hgmp.mrc.ac.uk>; from ableasby@hgmp.mrc.ac.uk on Wed, Aug 02, 2000 at 10:33:02AM +0100 References: <200008020933.KAA10553@bromine.hgmp.mrc.ac.uk> Message-ID: <20001031154658.M815@fling.sanbi.ac.za> ableasby at hgmp.mrc.ac.uk on 2000-08-02 (Wed) at 10:33:02 +0100: > > Well, it works for us anyway. Val and I have had a look on two > exceed setups, one where it failed and one where it worked. > As we suspected it was a trucolor problem where the failure > occurred. > > Go to the exceed configuration. Click on Screen Definition, then > set Server Visual to Pseudocolour and hopefully it'll work. It seems that this problem is not specific to Exceed. A user here recently encountered an identical problem using X-Win 32 (another X Server for Windows). The solution was identical (though I can't recall exactly where in the X-Win 32 configuration screens the change had to be made). -- Johann From ableasby at hgmp.mrc.ac.uk Tue Oct 31 16:35:05 2000 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Tue, 31 Oct 2000 16:35:05 GMT Subject: EMBOSS 1.7.0 Message-ID: <200010311635.QAA12918@tin.hgmp.mrc.ac.uk> NB: The default operation of -osf gcg has changed with 1.7.0 The same applies to the staden, plain, text & experiment formats. The problem with all the above formats is that if you retrieved multiple sequences they would all go into the same file. This would, of course, be meaningless. The strange thing is that that's precisely what we've decided to do in this release. Old behaviour for (e.g.) -osf gcg: The output filename would be ignored and EMBOSS would generate filenames automatically. This was confusing a lot of people.... especially as it wasn't really documented. To get it to have the same behaviour as all the other formats the switch -noossingle had to be used. New behaviour: It now recognises the output filename. This means that it is up to you to make sure you only retrieve single sequences. If you want to retrieve multiple sequences in GCG format you must send them to single files by putting -ossingle on the command line. At least the behaviour is now consistent and, if you're feeling perverse, you could use this feature for catenating sequences in plain format instead of pasteseq! ENTRET: This application is a bit like SEQRET but retrieves whole database entries in their original format. It works only with flatfiles (e.g. indexed by dbiflat) and is currently only implemented for EMBL & GenBank format databases. A long-standing problem of -slower and -supper only converting the first sequence in multi-sequence retrieval has been fixed. Alan