From markw at illuminae.com Wed Feb 2 04:08:59 2005 From: markw at illuminae.com (Mark Wilkinson) Date: Mon Mar 7 01:06:52 2005 Subject: tag does not fit model error 4.9t Message-ID: <41FF8D48.2060308@illuminae.com> Hi all! Yes, I'm still kicking around with AceDB :-) I'm experiencing a peculiarity that has me a bit befuddled. I did the following: 1) I have a models.wrm and a bunch of .ace files generated from a dump of the associated database. 2) I start up ACE (4.9t) and initiatlize a new database with this models.wrm file. 3) I start to read in the ACE files (b.t.w. why don't they all read in one after another like they used to?) 4) I get an error in my Protein class saying that tag DNA_homol does not fit model. 5) I look at the offending line in the .ace file and it is simply Protein : xxxx DNA_homol yyyy 6) I look at what is loaded into the database, and it has in fact been written into the DB! 7) I open the "offending" Protein record, and make a dump of *just* that record. 8) I look at the two .ace files side by side and they are 100% identical. How can it be that Ace can read in a record, claim that there is an error, read it in regardless, and then dump out exactly the same "erroneous" record? you'll have to trust me that the error message is incorrect,and that DNA_homol is, in fact, a valid tag in the model :-) Any advice is welcome!! Cheers all! Mark --- From edgrif at sanger.ac.uk Wed Feb 2 04:14:15 2005 From: edgrif at sanger.ac.uk (Ed Griffiths) Date: Mon Mar 7 01:06:52 2005 Subject: tag does not fit model error 4.9t References: <41FF8D48.2060308@illuminae.com> Message-ID: Mark, Several users reported this, if you update to 4.9v you should find the problem has gone away, sorry for the inconvenience. In point 3) you mention that the files don't read in automatically any more, can you just clarify what files/ where they are etc etc Ed > I'm experiencing a peculiarity that has me a bit befuddled. I did the > following: > > 1) I have a models.wrm and a bunch of .ace files generated from a dump > of the associated database. > 2) I start up ACE (4.9t) and initiatlize a new database with this > models.wrm file. > 3) I start to read in the ACE files (b.t.w. why don't they all read in > one after another like they used to?) > 4) I get an error in my Protein class saying that tag DNA_homol does > not fit model. > 5) I look at the offending line in the .ace file and it is simply > > Protein : xxxx > DNA_homol yyyy > > 6) I look at what is loaded into the database, and it has in fact been > written into the DB! > 7) I open the "offending" Protein record, and make a dump of *just* > that record. > 8) I look at the two .ace files side by side and they are 100% identical. > > How can it be that Ace can read in a record, claim that there is an > error, read it in regardless, and then dump out exactly the same > "erroneous" record? you'll have to trust me that the error message is > incorrect,and that DNA_homol is, in fact, a valid tag in the model :-) -- ------------------------------------------------------------------------ | Ed Griffiths, Acedb development, Informatics Group, | | Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, | | Hinxton, Cambridge CB10 1SA, UK | | | | email: edgrif@sanger.ac.uk Tel: +44-1223-494780 Fax: +44-1223-494919 | ------------------------------------------------------------------------ From markw at illuminae.com Fri Feb 4 02:36:43 2005 From: markw at illuminae.com (Mark Wilkinson) Date: Mon Mar 7 01:06:52 2005 Subject: tag does not fit model error 4.9t Message-ID: <4202BC75.7090202@illuminae.com> Hi Ed! Build 4.9v is not listed as a "stable release" (in fact, it isn't listed at all on the downloads page... the last supported release is 4.9t on the website, and the other versions listed don't pass all tests). Is it safe to run 4.9v as a production db? what I meant by "doesn't read files automatically" is that in both xace and tace I want to be able to say: parse dump_2005-02-03* and get it to read them all in, rather than having to name them one-by-one. I recall that, in xace, it used to be only necessary to double-click the first one and the rest would get sucked in automatically. I guess that isn't a particular nice behaviour from a GUI, but from a text interface is seems friendly! Let me know about 4.9v, and if it is stable then I'll happily upgrade. Cheers all!! Mark --- From edgrif at sanger.ac.uk Fri Feb 4 02:49:27 2005 From: edgrif at sanger.ac.uk (Ed Griffiths) Date: Mon Mar 7 01:06:52 2005 Subject: tag does not fit model error 4.9t References: <4202BC75.7090202@illuminae.com> Message-ID: Mark, > Build 4.9v is not listed as a "stable release" (in fact, it isn't listed > at all on the downloads page... the last supported release is 4.9t on > the website, and the other versions listed don't pass all tests). Is it > safe to run 4.9v as a production db? Sorry, I meant to say 4.9z, agh, what an idiot. Don't worry about the failing tests they are to do with some new tests/functions we have incorporated and the percentage will go back up to a 100 once 4.9z becomes the stable release. > what I meant by "doesn't read files automatically" is that in both xace > and tace I want to be able to say: > > parse dump_2005-02-03* > > and get it to read them all in, rather than having to name them one-by-one. > > I recall that, in xace, it used to be only necessary to double-click the > first one and the rest would get sucked in automatically. I guess that > isn't a particular nice behaviour from a GUI, but from a text interface > is seems friendly! Just to be clear, are you saying that tace used to do this and now it doesn't ? If so I will restore the behaviour, I could add it to tace but it will have to go into the list of stuff to be done ;-) Ed -- ------------------------------------------------------------------------ | Ed Griffiths, Acedb development, Informatics Group, | | Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, | | Hinxton, Cambridge CB10 1SA, UK | | | | email: edgrif@sanger.ac.uk Tel: +44-1223-494780 Fax: +44-1223-494919 | ------------------------------------------------------------------------ From krb at sanger.ac.uk Mon Feb 7 17:00:47 2005 From: krb at sanger.ac.uk (Keith Bradnam) Date: Mon Mar 7 01:06:52 2005 Subject: Instructions for installing acedb on Mac OS X 10.3 Message-ID: I found that I needed to tweak the instructions given at: http://www.acedb.org/Software/Downloads/supported.shtml in order to get xace to work properly on Panther (10.3). This might be because the acedb debian package was built using Jaguar (10.2) and there may be some subtle library differences between the two releases. Full details are below and assume that you know nothing (well nearly nothing) and have done nothing. Regards, Keith INSTALLATION INSTRUCTIONS FOR INSTALLING ACEDB BINARIES ------------------------------------------------------- NOTE 1: This protocol has only been tested on Mac OS X 10.3 (Panther) and with version 4.9t of the acedb binaries (xace, tace, giface etc.). Later versions of acedb may require changes (most likely to install other dependent packages). NOTE 2: Fink provides a few different ways of installing packages. I initially used the 'fink install' method but discovered that fink will insist that the xfree86 package needs to be installed when installing gtk+. This is not true if you have Apple's X11 application already installed. I found that the 'apt-get install' command gets around this. 1) Install fink (http://fink.sourceforge.net/). At time of writing this is the only successful method I have found to install acedb. If you have a /sw directory on your machine (at the top level) then fink is most likely already installed. 2) Each user on the system needs to configure their path so that they can 'see' the /sw/bin directory where any applications installed by fink will be located. This can simply be done by running a fink shell configuration script (this script will change your .profile file): . /sw/bin/init.sh Note that running this script will not affect the X11 terminal application as this does not read a users .profile file. You will either have to manually run this command in each X11 terminal or add -ls as an command line option for xterm (go to 'Cutomize' in the Applications menu. This forces the terminal to read the login shell profile (but note that this still doesn't happen in the *first* terminal window that automatically launches as part of X11). 3) Make sure that the apt-get command (part of fink) knows about the latest set of available packages (this is not strictly necessary but is good practice): sudo apt-get update 4) Install Mac OS X developer tools. Without these Mac OS X does not have a C compiler which can be used by fink for installing some packages. 5) Install readline package if not already present (this is required by acedb). You can check by typing the following in a terminal window: fink list readline A lower case 'i' at the start of the output indicates that it exists and is already installed. If no 'i' appears then install readline by typing: sudo apt-get install readline The install routine may request that other dependent packages need to be installed. Answer 'Y' when prompted to do so to install these. 6) Install gtk+. Again you can see if this installed by typing: fink list gtk+ If it needs to be installed then run: sudo apt-get install gtk+ 7) Now download the acedb debian package from the link on: http://www.acedb.org/Software/Downloads/supported.shtml The actual URL will change with each version, but here is an example: http://www.acedb.org/Software/Downloads/MACOS/ACEDB-MACOSX.4.9t.tar.gz This package should unpack to a folder called 'ACEDB-MACOSX.4.9t.tar.gz Folder' and in this folder will be a file called: acedb_4.9t-1_darwin-powerpc.deb Again, the actual name will be release specific. In that directory you now need to run: sudo dpkg -i acedb_4.9t-1_darwin-powerpc.deb This should end up adding tace, xace, giface etc. binaries to /sw/bin. 8) Normally this should be all that is needed, but there still seems to be a problem with one dependent package missing (dlcompat-shlibs). Try running xace on the command line of an X11 terminal and if it complains, install this extra package: sudo apt-get install dlcomat-shlibs That should be it, you should now be able to launch xace (you will still need a database with valid data in, but even without a database you should see an xace error popup message). ~ Keith Bradnam - WormBase group: http://www.wormbase.org/ ~ ~ The Wellcome Trust Sanger Institute, ~ Hinxton, Cambridge, CB10 1SA, UK. Tel: 01223 494922 From rnc at sanger.ac.uk Tue Feb 8 04:52:03 2005 From: rnc at sanger.ac.uk (Rob Clack) Date: Mon Mar 7 01:06:52 2005 Subject: Instructions for installing acedb on Mac OS X 10.3 References: Message-ID: <42088BA9.6010003@sanger.ac.uk> Keith, this is a great help! I've posted your email verbatim on the website with a link from the Mac download section. When I get a chance, I'll straighten it all out, but it seemed more important to just get it out there asap. Thanks again. Rob -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Rob Clack Acedb Development, Informatics Group email: rnc@sanger.ac.uk Wellcome Trust Sanger Institute Tel: +44 1223 494883 Wellcome Trust Genome Campus Fax: +44 1223 494919 Hinxton Cambridge CB10 1SA From keil2000 at yahoo.com Thu Feb 24 04:13:25 2005 From: keil2000 at yahoo.com (Al Zhao) Date: Mon Mar 7 01:06:52 2005 Subject: Novice Need Help Message-ID: <20050223223002.58029.qmail@web90108.mail.scd.yahoo.com> Hello everyone, I am new to AceDb. Can someone help me? I need to know how to draw the Map of the DNA sequence. Also from GenBank, I noticed the sequences of some genes are from mRNA. Is there a database out there I could extract the DNA Sequence for those genes? Thank you very much. Al __________________________________ Do you Yahoo!? Yahoo! Mail - Easier than ever with enhanced search. Learn more. http://info.mail.yahoo.com/mail_250 --- From edgrif at sanger.ac.uk Thu Feb 24 04:22:03 2005 From: edgrif at sanger.ac.uk (Ed Griffiths) Date: Mon Mar 7 01:06:52 2005 Subject: Novice Need Help References: <20050223223002.58029.qmail@web90108.mail.scd.yahoo.com> Message-ID: Al Zhao, > Hello everyone, I am new to AceDb. Can someone help > me? I need to know how to draw the Map of the DNA > sequence. Also from GenBank, I noticed the sequences > of some genes are from mRNA. Is there a database out > there I could extract the DNA Sequence for those > genes? Thank you very much. Please can you describe what data you have and how you want to view it in a bit more detail please ? What sequence are you looking at, which genes etc. etc. Ed -- ------------------------------------------------------------------------ | Ed Griffiths, Acedb development, Informatics Group, | | Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, | | Hinxton, Cambridge CB10 1SA, UK | | | | email: edgrif@sanger.ac.uk Tel: +44-1223-494780 Fax: +44-1223-494919 | ------------------------------------------------------------------------