From d.counsell at hgmp.mrc.ac.uk Mon Aug 19 10:16:44 2002 From: d.counsell at hgmp.mrc.ac.uk (Damian Counsell) Date: Mon, 19 Aug 2002 15:16:44 +0100 Subject: EDP Update Message-ID: <20020819151644.D32049@dev4.hgmp.mrc.ac.uk> Dear All Latest update to EDP page at: http://www.hgmp.mrc.ac.uk/~dcounsel/EDP/EMBOSS_documentation.html . all the best Damian -- Damian COUNSELL email: d.counsell at hgmp.mrc.ac.uk MRC Human Genome Mapping Project RC phone: +44 (0)1223 494500 Cambridge CB10 1SB direct: +44 (0)1223 494585 http://www.hgmp.mrc.ac.uk/~dcounsel/ fax: +44 (0)1223 494512 From gbottu at ben.vub.ac.be Mon Aug 26 11:52:32 2002 From: gbottu at ben.vub.ac.be (Guy Bottu) Date: Mon, 26 Aug 2002 17:52:32 +0200 (CEST) Subject: remarks about ACD syntax Message-ID: <200208261552.RAA0001128135@ben.vub.ac.be> from : BEN Dear colleagues, I have started to port under EMBOSS some local developements we had under GCG at the BEN site. I wrote some ACD files (under EMBOSS 2.4.1) and I bumped on some limitations of the syntax. - the return value of a "list" or "select" cannot be used in computations for other fields. Yet, this would be veru useful. E.g. for integrating BLAST under EMBOSS you could first have a select with blastn/blastp/blastx/tblastn/tblastx that would control the default values of all the other parameters. - some parameters can be "required" or not, depending on other parameters. When a parameter is sometimes required however, it is necessary to provide a default value, otherwise an error message will appear when you run the program via selections that do not involve that parameter. The ACD documentation mentions a "missing" attribute, but this seems not to work. - a parameter of the type "outfile" leads always to the creation of a file, even when the outfile is optional. An example : when you run dan -plot, an empty file xxx.dan is created. Am I wrong ? And if not, can we expect a future version with more flexible syntax ? Sincerely, Guy Bottu From gbottu at ben.vub.ac.be Mon Aug 26 11:52:34 2002 From: gbottu at ben.vub.ac.be (Guy Bottu) Date: Mon, 26 Aug 2002 17:52:34 +0200 (CEST) Subject: question about EMBOSS manual Message-ID: <200208261552.RAA0001128235@ben.vub.ac.be> from : BEN Dear colleagues, I have started to port under EMBOSS some local developements we had under GCG at the BEN site. I would like to write program documentation files (txt and html). I read the on-line documentation at http://www.hgmp.mrc.ac.uk/Software/EMBOSS/Doc/programdoc.html but did not get much wiser. Therefore my questions : must the txt files respect a certain standard ? Is there a tool make the html files ? Guy Bottu From ableasby at hgmp.mrc.ac.uk Mon Aug 26 12:09:52 2002 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Mon, 26 Aug 2002 17:09:52 +0100 (BST) Subject: remarks about ACD syntax Message-ID: <200208261609.RAA25579@bromine.hgmp.mrc.ac.uk> Guy, It is possible to use the values of list datatypes. As an example you could look at the use of 'type' in prophecy.acd There is the attribute 'nullok' (as in nullok: Y) to specify that an outfile needn't be created. I suppose we could extend this attribute to other datatypes to get around the default requirement but haven't yet found the need. Adding a default value isn't that much effort after all. Cheers Alan From ableasby at hgmp.mrc.ac.uk Mon Aug 26 12:13:51 2002 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Mon, 26 Aug 2002 17:13:51 +0100 (BST) Subject: question about EMBOSS manual Message-ID: <200208261613.RAA25720@bromine.hgmp.mrc.ac.uk> That's good news wrt the porting. As to documentation, Gary can inform you better than I wrt the current ideals. The EDP (EMBOSS documentation project) is currently developing tools for creating documentation as we are moving towards use of docbook. Cheers Alan From brooks at embl-grenoble.fr Mon Aug 26 13:44:06 2002 From: brooks at embl-grenoble.fr (Brooks Mark) Date: Mon, 26 Aug 2002 19:44:06 +0200 Subject: Saving multiple sequences contained in a linked list. References: <200208261609.RAA25579@bromine.hgmp.mrc.ac.uk> Message-ID: <3D6A68E6.2EBB5917@embl-grenoble.fr> A quick teaser for those interested in testing their grey matter... Can anyone spot the mistake in the following function please? Actually, I can't do it, that's why I'm asking ;-)! ...actually, there may be many mistakes, but as I try and traverse this linked list (by moving to list->next) and save each sequence in turn, all I do in the end is save the first sequence as many times as there are items in the list. Here is the offending code ===================================================== void real_export_all(GtkWidget * app, gchar * filename) { GList *list; AjPStr seqfilename, seq_formatstr; AjPSeqout seqoutname; SeqListItem *seq_list_item; GNode *node; seqfilename = ajStrNewC("/tmp/wibble.fas"); seq_formatstr = ajStrNewC("fasta"); seqoutname = ajSeqoutNew(); (void) ajSeqFileNewOut(seqoutname, seqfilename); for (list = trees ; list != NULL ; list = list->next){ node = trees->data; seq_list_item = node->data; (void) ajSeqOutSetFormat(seqoutname, seq_formatstr); ajSeqAllWrite(seqoutname, seq_list_item->seq); } (void) ajSeqWriteClose(seqoutname); return; } ======================================== and a SeqListItem is just this (for now) ======================================== typedef struct _SeqListItem SeqListItem; struct _SeqListItem { AjPSeq seq; gint frame; }; ========================================== "trees" is a global variable (ugh) of type GList. ========================================== If you feel you need more information, you can always browse the cvs for the entire program at the Sourceforge page.... http://sourceforge.net/projects/gnome-emboss/ ........to browse the CVS... http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/gnome-emboss ........to see it in action at the web page... http://gnome-emboss.sourceforge.net/ (which is very incomplete!). or to download and try and build the thing (I think ssh is required, but not sure on this one) cvs -d:pserver:anonymous at cvs.gnome-emboss.sourceforge.net:/cvsroot/gnome-emboss login cvs -z3 -d:pserver:anonymous at cvs.gnome-emboss.sourceforge.net:/cvsroot/gnome-emboss co gnome-emboss (Requires libxml, gnome, glade, libglade, auto(make,conf, etc.), the usual suspects). Any comments on anything related are more than welcome. Sorry if this is a stupid question- I'm not great at programming yet! Mark. P.S. Yes, it is a rip off of GDE, without as much functionality. P.P.S. By the way, the program's name is _not_ going to stay as "Gnome-EMBOSS" (I hope it doesn't cause offence in Cambs. that I even use EMBOSS in the name) for long; we're having a competition here to come up with something better. An average user would have no idea what Gnome-EMBOSS would do! The leading contender for the name is currently: "DNAvigator" (despite potential confusion with Netscape Navigator, this is the best we've done). If you have something better you could win a crate of beer..... -- Mark Brooks, EMBL Grenoble Outstation, 6, rue Jules Horowitz, BP181 38042 Grenoble Cedex 9, France. Tel: + (0)4 76 20 72 85 From d.counsell at hgmp.mrc.ac.uk Mon Aug 26 14:46:11 2002 From: d.counsell at hgmp.mrc.ac.uk (Damian Counsell) Date: Mon, 26 Aug 2002 19:46:11 +0100 Subject: question about EMBOSS manual In-Reply-To: <200208261552.RAA0001128235@ben.vub.ac.be>; from gbottu@ben.vub.ac.be on Mon, Aug 26, 2002 at 05:52:34PM +0200 References: <200208261552.RAA0001128235@ben.vub.ac.be> Message-ID: <20020826194611.A975@hgmp.mrc.ac.uk> Guy! * Guy Bottu [020826 16:53]: > from : BEN > > I have started to port under EMBOSS some local developements we had under GCG at > the BEN site. I would like to write program documentation files (txt and html). Are you looking for a job any time soon? ;-) > I read the on-line documentation at > http://www.hgmp.mrc.ac.uk/Software/EMBOSS/Doc/programdoc.html but > did not get much wiser. Therefore my questions : must the txt files > respect a certain standard ? Ooh, don't get me started... As Alan pointed out, enhancing the documentation is definitely a priority at the moment and XML (DocBook) will be the new standard. For the latest news go here: http://www.hgmp.mrc.ac.uk/~dcounsel/EDP/EMBOSS_documentation.html and for Terry Stewart's documentation on the new documentation go here: http://www.hgmp.mrc.ac.uk/~tjstewar/EMBOSS/EmbossDocumentation.html . With the arrival of this page EMBOSS introduces a variation on recursive acronyms by telling its developers to RTFMM... Here's the template: http://www.hgmp.mrc.ac.uk/~tjstewar/EMBOSS/EmbossTemplate.html > Is there a tool make the html files ? There's a tool to make the XML files: http://www.xmlmind.com/xmleditor/ which you can use in conjunction with Terry's stylesheets to produce HTML or with the OpenJade package to produce LaTeX, PDF or RTF. all the best Damian -- Damian COUNSELL email: d.counsell at hgmp.mrc.ac.uk MRC Human Genome Mapping Project RC phone: +44 (0)1223 494500 Cambridge CB10 1SB direct: +44 (0)1223 494585 http://www.hgmp.mrc.ac.uk/~dcounsel/ fax: +44 (0)1223 494512 From peter.rice at uk.lionbioscience.com Tue Aug 27 05:21:29 2002 From: peter.rice at uk.lionbioscience.com (Peter Rice) Date: Tue, 27 Aug 2002 10:21:29 +0100 Subject: remarks about ACD syntax References: <200208261552.RAA0001128135@ben.vub.ac.be> Message-ID: <3D6B4499.7060604@uk.lionbioscience.com> Guy Bottu wrote: > - the return value of a "list" or "select" cannot be used in computations for > other fields. Yet, this would be veru useful. E.g. for integrating BLAST under > EMBOSS you could first have a select with blastn/blastp/blastx/tblastn/tblastx > that would control the default values of all the other parameters. You can use the value. The easy way to test what the values are is to write a new ACD file, with the value in the prompt for another ACD option (so you can see it). For example: % cat guy.acd appl: guy [ doc: "Test" group: "Testing" ] select: program [ value: "blastn/blastp/blastx/tblastn/tblastx" delim: "/" required: "Y" info: "Blast program name" ] string: testa [ info: "program '$(program)'" required: "Y" ] string: testb [ info: "comparison type" required: "Y" default: "@($(program) = blastn: N/N blastp: P/P blastx: X/P tblastn: P/X tblastx: X/X)" ] % acdc guy Test 1 : blastn 2 : blastp 3 : blastx 4 : tblastn 5 : tblastx Blast program name: 3 program 'blastx': comparison type [X/P]: If you need other information, for example with multiple selected values, we could add new "calculated" attributes for list or select. One problem with these ACD values, of course, is that they are hard to use when generating GUI interfaces to EMBOSS programs. > - some parameters can be "required" or not, depending on other parameters. When > a parameter is sometimes required however, it is necessary to provide a default > value, otherwise an error message will appear when you run the program via > selections that do not involve that parameter. The ACD documentation mentions a > "missing" attribute, but this seems not to work. Can you give an example? Usually this problem is programs that fail to call "ajAcdGetXxxx" for a parameter so it gives a "never used" warning message. These cases should be fixed. > - a parameter of the type "outfile" leads always to the creation of a file, even > when the outfile is optional. An example : when you run dan -plot, an empty file > xxx.dan is created. The report file (report, align or outfile) is created by ACD processing before the program runs. Maybe we need an attribute to say the file is not needed, calculated from $(graph). Does this sound reasonable? regards, Peter Rice -- ------------------------------------------------ Peter Rice, LION Bioscience Ltd, Cambridge, UK peter.rice at uk.lionbioscience.com +44 1223 224723 From gbottu at ben.vub.ac.be Wed Aug 28 07:56:48 2002 From: gbottu at ben.vub.ac.be (gbottu at ben.vub.ac.be) Date: Wed, 28 Aug 2002 13:56:48 +0200 (CEST) Subject: ACD not always required parameters Message-ID: <200208281156.NAA0001307743@blackjack.ben.vub.ac.be> Dear Peter, Thanks ! Your reply and the one by Alan have helped me a lot. I wonder why at my first attempt I could not use the result of a list in a computation, I must have done something wrong. Remains the problem of the required parameters. I send an example as attachment. You will note that the fields "userdb" and "userfastadb" have no reasonable default. The one I had to add is an awfull hack. But delete default and run "acdc fasta", you will get an error. Sincerely, Guy Bottu -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/octet-stream Size: 7822 bytes Desc: fasta.acd Url : http://lists.open-bio.org/pipermail/emboss-dev/attachments/20020828/7ffb7dcf/attachment.obj From peter.rice at uk.lionbioscience.com Wed Aug 28 08:20:21 2002 From: peter.rice at uk.lionbioscience.com (Peter Rice) Date: Wed, 28 Aug 2002 13:20:21 +0100 Subject: ACD not always required parameters References: <200208281156.NAA0001307743@blackjack.ben.vub.ac.be> Message-ID: <3D6CC005.3060705@uk.lionbioscience.com> gbottu at ben.vub.ac.be wrote: > Remains the problem of the required parameters. I send an > example as attachment. The data type is seqall. This will need a value. No value (empty default) means it tries to read nothing. It is a seqall (or sequence or seqset) that needs a value, the 'required' part is not important ... except of course if it is 'required' the user will be prompted. > You will note that the fields "userdb" and "userfastadb" have no reasonable > default. The one I had to add is an awfull hack. But delete default and run > "acdc fasta", you will get an error. The big problem here is trying to fit all the FASTA programs into one ACD file, instead of using 9 files. I did consider some time back extending ACD syntax to cover launching external applications with an ACD interface. There is an outline syntax definition including additional validation for (for example) blast gap penalties. The tricky part is testing the input is valid where it is a strange database (blast for example) before launching the application. Can anyone help with defining requirements for blast/fasta/etc. regards, Peter -- ------------------------------------------------ Peter Rice, LION Bioscience Ltd, Cambridge, UK peter.rice at uk.lionbioscience.com +44 1223 224723 From gwilliam at hgmp.mrc.ac.uk Wed Aug 28 10:43:47 2002 From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522) Date: Wed, 28 Aug 2002 15:43:47 +0100 Subject: automatic documentation from qatest data Message-ID: <3D6CE1A3.7B34@hgmp.mrc.ac.uk> I think I've got a workable system for automatically producing documentation of an application's Usage, Input files and Output files sections. The data for these sections is derived from the qatest.dat file. For examples, see: http://www.hgmp.mrc.ac.uk/Software/EMBOSS/Apps/antigenic.html http://www.hgmp.mrc.ac.uk/Software/EMBOSS/Apps/backtranseq.html http://www.hgmp.mrc.ac.uk/Software/EMBOSS/Apps/plotorf.html Comments please. Do the output gif files look OK you you in the plotorf documentation? Thanks, Gary -- 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 gbottu at ben.vub.ac.be Thu Aug 29 09:21:58 2002 From: gbottu at ben.vub.ac.be (gbottu at ben.vub.ac.be) Date: Thu, 29 Aug 2002 15:21:58 +0200 (CEST) Subject: fasta and ACD not always required parameters Message-ID: <200208291321.PAA0001348869@blackjack.vub.ac.be> > The data type is seqall. This will need a value. No value (empty default) > means it tries to read nothing. > > It is a seqall (or sequence or seqset) that needs a value, the 'required' > part is not important ... except of course if it is 'required' the user > will be prompted. Yes, you're right. The parameter "required" has nothing to do with it. The problem is that there are cases when where you sometimes need to read in a sequence and sometimes not, depending on the circumstances, and that there is obviously no good default here. The parameter "nullok" works for "infile" and "outfile". Maybe a good idea is to make "nullok" (or "missing" or whatever) work for any data type. > The big problem here is trying to fit all the FASTA programs into one ACD file, > instead of using 9 files. > > I did consider some time back extending ACD syntax to cover launching > external applications with an ACD interface. There is an outline syntax > definition including additional validation for (for example) blast gap > penalties. The tricky part is testing the input is valid where it is a > strange database (blast for example) before launching the application. > > Can anyone help with defining requirements for blast/fasta/etc. Making all fastA or BLAST options work in one rather than in 9 resp. 5 is not a problem, since I did it well. The problem is with the input of the search set. Since I did not try to "embossify" the original program but only wrote a wrapper application in EMBOSS, I had to consider 3 cases : 1) standard search set : the program uses an existing databank installed by BEN (in some cases a fastA "library" file or a BLAST .nal/.pal file is used) 2) user defined search set : the wrapper reads in a "seqall" and generates in /tmp a temporary databank in fastA or BLAST format. This could in principle be used always, but you understand we wouldn't like to do it for embl:* 3) user provided databank in fastA or BLAST format : used directly by the program. The wrapper does some testing before launching the program. For fastA the databank is read in as ftp::xxx and then typed with ajSeqTypeNuc/ajSeqTypeProt, for BLAST very crudely just the existence of three files with appropriate extension is tested. I admit that all this is tinkering rather than an elegant solution. For an in depth solution the programs themselves should be changed and/or several new features added to EMBOSS. In the meantime, just extending the "nullok" parameter to all data types should make me happy. Sincerely, Guy Bottu From d.counsell at hgmp.mrc.ac.uk Mon Aug 19 14:16:44 2002 From: d.counsell at hgmp.mrc.ac.uk (Damian Counsell) Date: Mon, 19 Aug 2002 15:16:44 +0100 Subject: EDP Update Message-ID: <20020819151644.D32049@dev4.hgmp.mrc.ac.uk> Dear All Latest update to EDP page at: http://www.hgmp.mrc.ac.uk/~dcounsel/EDP/EMBOSS_documentation.html . all the best Damian -- Damian COUNSELL email: d.counsell at hgmp.mrc.ac.uk MRC Human Genome Mapping Project RC phone: +44 (0)1223 494500 Cambridge CB10 1SB direct: +44 (0)1223 494585 http://www.hgmp.mrc.ac.uk/~dcounsel/ fax: +44 (0)1223 494512 From gbottu at ben.vub.ac.be Mon Aug 26 15:52:32 2002 From: gbottu at ben.vub.ac.be (Guy Bottu) Date: Mon, 26 Aug 2002 17:52:32 +0200 (CEST) Subject: remarks about ACD syntax Message-ID: <200208261552.RAA0001128135@ben.vub.ac.be> from : BEN Dear colleagues, I have started to port under EMBOSS some local developements we had under GCG at the BEN site. I wrote some ACD files (under EMBOSS 2.4.1) and I bumped on some limitations of the syntax. - the return value of a "list" or "select" cannot be used in computations for other fields. Yet, this would be veru useful. E.g. for integrating BLAST under EMBOSS you could first have a select with blastn/blastp/blastx/tblastn/tblastx that would control the default values of all the other parameters. - some parameters can be "required" or not, depending on other parameters. When a parameter is sometimes required however, it is necessary to provide a default value, otherwise an error message will appear when you run the program via selections that do not involve that parameter. The ACD documentation mentions a "missing" attribute, but this seems not to work. - a parameter of the type "outfile" leads always to the creation of a file, even when the outfile is optional. An example : when you run dan -plot, an empty file xxx.dan is created. Am I wrong ? And if not, can we expect a future version with more flexible syntax ? Sincerely, Guy Bottu From gbottu at ben.vub.ac.be Mon Aug 26 15:52:34 2002 From: gbottu at ben.vub.ac.be (Guy Bottu) Date: Mon, 26 Aug 2002 17:52:34 +0200 (CEST) Subject: question about EMBOSS manual Message-ID: <200208261552.RAA0001128235@ben.vub.ac.be> from : BEN Dear colleagues, I have started to port under EMBOSS some local developements we had under GCG at the BEN site. I would like to write program documentation files (txt and html). I read the on-line documentation at http://www.hgmp.mrc.ac.uk/Software/EMBOSS/Doc/programdoc.html but did not get much wiser. Therefore my questions : must the txt files respect a certain standard ? Is there a tool make the html files ? Guy Bottu From ableasby at hgmp.mrc.ac.uk Mon Aug 26 16:09:52 2002 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Mon, 26 Aug 2002 17:09:52 +0100 (BST) Subject: remarks about ACD syntax Message-ID: <200208261609.RAA25579@bromine.hgmp.mrc.ac.uk> Guy, It is possible to use the values of list datatypes. As an example you could look at the use of 'type' in prophecy.acd There is the attribute 'nullok' (as in nullok: Y) to specify that an outfile needn't be created. I suppose we could extend this attribute to other datatypes to get around the default requirement but haven't yet found the need. Adding a default value isn't that much effort after all. Cheers Alan From ableasby at hgmp.mrc.ac.uk Mon Aug 26 16:13:51 2002 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Mon, 26 Aug 2002 17:13:51 +0100 (BST) Subject: question about EMBOSS manual Message-ID: <200208261613.RAA25720@bromine.hgmp.mrc.ac.uk> That's good news wrt the porting. As to documentation, Gary can inform you better than I wrt the current ideals. The EDP (EMBOSS documentation project) is currently developing tools for creating documentation as we are moving towards use of docbook. Cheers Alan From brooks at embl-grenoble.fr Mon Aug 26 17:44:06 2002 From: brooks at embl-grenoble.fr (Brooks Mark) Date: Mon, 26 Aug 2002 19:44:06 +0200 Subject: Saving multiple sequences contained in a linked list. References: <200208261609.RAA25579@bromine.hgmp.mrc.ac.uk> Message-ID: <3D6A68E6.2EBB5917@embl-grenoble.fr> A quick teaser for those interested in testing their grey matter... Can anyone spot the mistake in the following function please? Actually, I can't do it, that's why I'm asking ;-)! ...actually, there may be many mistakes, but as I try and traverse this linked list (by moving to list->next) and save each sequence in turn, all I do in the end is save the first sequence as many times as there are items in the list. Here is the offending code ===================================================== void real_export_all(GtkWidget * app, gchar * filename) { GList *list; AjPStr seqfilename, seq_formatstr; AjPSeqout seqoutname; SeqListItem *seq_list_item; GNode *node; seqfilename = ajStrNewC("/tmp/wibble.fas"); seq_formatstr = ajStrNewC("fasta"); seqoutname = ajSeqoutNew(); (void) ajSeqFileNewOut(seqoutname, seqfilename); for (list = trees ; list != NULL ; list = list->next){ node = trees->data; seq_list_item = node->data; (void) ajSeqOutSetFormat(seqoutname, seq_formatstr); ajSeqAllWrite(seqoutname, seq_list_item->seq); } (void) ajSeqWriteClose(seqoutname); return; } ======================================== and a SeqListItem is just this (for now) ======================================== typedef struct _SeqListItem SeqListItem; struct _SeqListItem { AjPSeq seq; gint frame; }; ========================================== "trees" is a global variable (ugh) of type GList. ========================================== If you feel you need more information, you can always browse the cvs for the entire program at the Sourceforge page.... http://sourceforge.net/projects/gnome-emboss/ ........to browse the CVS... http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/gnome-emboss ........to see it in action at the web page... http://gnome-emboss.sourceforge.net/ (which is very incomplete!). or to download and try and build the thing (I think ssh is required, but not sure on this one) cvs -d:pserver:anonymous at cvs.gnome-emboss.sourceforge.net:/cvsroot/gnome-emboss login cvs -z3 -d:pserver:anonymous at cvs.gnome-emboss.sourceforge.net:/cvsroot/gnome-emboss co gnome-emboss (Requires libxml, gnome, glade, libglade, auto(make,conf, etc.), the usual suspects). Any comments on anything related are more than welcome. Sorry if this is a stupid question- I'm not great at programming yet! Mark. P.S. Yes, it is a rip off of GDE, without as much functionality. P.P.S. By the way, the program's name is _not_ going to stay as "Gnome-EMBOSS" (I hope it doesn't cause offence in Cambs. that I even use EMBOSS in the name) for long; we're having a competition here to come up with something better. An average user would have no idea what Gnome-EMBOSS would do! The leading contender for the name is currently: "DNAvigator" (despite potential confusion with Netscape Navigator, this is the best we've done). If you have something better you could win a crate of beer..... -- Mark Brooks, EMBL Grenoble Outstation, 6, rue Jules Horowitz, BP181 38042 Grenoble Cedex 9, France. Tel: + (0)4 76 20 72 85 From d.counsell at hgmp.mrc.ac.uk Mon Aug 26 18:46:11 2002 From: d.counsell at hgmp.mrc.ac.uk (Damian Counsell) Date: Mon, 26 Aug 2002 19:46:11 +0100 Subject: question about EMBOSS manual In-Reply-To: <200208261552.RAA0001128235@ben.vub.ac.be>; from gbottu@ben.vub.ac.be on Mon, Aug 26, 2002 at 05:52:34PM +0200 References: <200208261552.RAA0001128235@ben.vub.ac.be> Message-ID: <20020826194611.A975@hgmp.mrc.ac.uk> Guy! * Guy Bottu [020826 16:53]: > from : BEN > > I have started to port under EMBOSS some local developements we had under GCG at > the BEN site. I would like to write program documentation files (txt and html). Are you looking for a job any time soon? ;-) > I read the on-line documentation at > http://www.hgmp.mrc.ac.uk/Software/EMBOSS/Doc/programdoc.html but > did not get much wiser. Therefore my questions : must the txt files > respect a certain standard ? Ooh, don't get me started... As Alan pointed out, enhancing the documentation is definitely a priority at the moment and XML (DocBook) will be the new standard. For the latest news go here: http://www.hgmp.mrc.ac.uk/~dcounsel/EDP/EMBOSS_documentation.html and for Terry Stewart's documentation on the new documentation go here: http://www.hgmp.mrc.ac.uk/~tjstewar/EMBOSS/EmbossDocumentation.html . With the arrival of this page EMBOSS introduces a variation on recursive acronyms by telling its developers to RTFMM... Here's the template: http://www.hgmp.mrc.ac.uk/~tjstewar/EMBOSS/EmbossTemplate.html > Is there a tool make the html files ? There's a tool to make the XML files: http://www.xmlmind.com/xmleditor/ which you can use in conjunction with Terry's stylesheets to produce HTML or with the OpenJade package to produce LaTeX, PDF or RTF. all the best Damian -- Damian COUNSELL email: d.counsell at hgmp.mrc.ac.uk MRC Human Genome Mapping Project RC phone: +44 (0)1223 494500 Cambridge CB10 1SB direct: +44 (0)1223 494585 http://www.hgmp.mrc.ac.uk/~dcounsel/ fax: +44 (0)1223 494512 From peter.rice at uk.lionbioscience.com Tue Aug 27 09:21:29 2002 From: peter.rice at uk.lionbioscience.com (Peter Rice) Date: Tue, 27 Aug 2002 10:21:29 +0100 Subject: remarks about ACD syntax References: <200208261552.RAA0001128135@ben.vub.ac.be> Message-ID: <3D6B4499.7060604@uk.lionbioscience.com> Guy Bottu wrote: > - the return value of a "list" or "select" cannot be used in computations for > other fields. Yet, this would be veru useful. E.g. for integrating BLAST under > EMBOSS you could first have a select with blastn/blastp/blastx/tblastn/tblastx > that would control the default values of all the other parameters. You can use the value. The easy way to test what the values are is to write a new ACD file, with the value in the prompt for another ACD option (so you can see it). For example: % cat guy.acd appl: guy [ doc: "Test" group: "Testing" ] select: program [ value: "blastn/blastp/blastx/tblastn/tblastx" delim: "/" required: "Y" info: "Blast program name" ] string: testa [ info: "program '$(program)'" required: "Y" ] string: testb [ info: "comparison type" required: "Y" default: "@($(program) = blastn: N/N blastp: P/P blastx: X/P tblastn: P/X tblastx: X/X)" ] % acdc guy Test 1 : blastn 2 : blastp 3 : blastx 4 : tblastn 5 : tblastx Blast program name: 3 program 'blastx': comparison type [X/P]: If you need other information, for example with multiple selected values, we could add new "calculated" attributes for list or select. One problem with these ACD values, of course, is that they are hard to use when generating GUI interfaces to EMBOSS programs. > - some parameters can be "required" or not, depending on other parameters. When > a parameter is sometimes required however, it is necessary to provide a default > value, otherwise an error message will appear when you run the program via > selections that do not involve that parameter. The ACD documentation mentions a > "missing" attribute, but this seems not to work. Can you give an example? Usually this problem is programs that fail to call "ajAcdGetXxxx" for a parameter so it gives a "never used" warning message. These cases should be fixed. > - a parameter of the type "outfile" leads always to the creation of a file, even > when the outfile is optional. An example : when you run dan -plot, an empty file > xxx.dan is created. The report file (report, align or outfile) is created by ACD processing before the program runs. Maybe we need an attribute to say the file is not needed, calculated from $(graph). Does this sound reasonable? regards, Peter Rice -- ------------------------------------------------ Peter Rice, LION Bioscience Ltd, Cambridge, UK peter.rice at uk.lionbioscience.com +44 1223 224723 From gbottu at ben.vub.ac.be Wed Aug 28 11:56:48 2002 From: gbottu at ben.vub.ac.be (gbottu at ben.vub.ac.be) Date: Wed, 28 Aug 2002 13:56:48 +0200 (CEST) Subject: ACD not always required parameters Message-ID: <200208281156.NAA0001307743@blackjack.ben.vub.ac.be> Dear Peter, Thanks ! Your reply and the one by Alan have helped me a lot. I wonder why at my first attempt I could not use the result of a list in a computation, I must have done something wrong. Remains the problem of the required parameters. I send an example as attachment. You will note that the fields "userdb" and "userfastadb" have no reasonable default. The one I had to add is an awfull hack. But delete default and run "acdc fasta", you will get an error. Sincerely, Guy Bottu -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/octet-stream Size: 7822 bytes Desc: fasta.acd URL: From peter.rice at uk.lionbioscience.com Wed Aug 28 12:20:21 2002 From: peter.rice at uk.lionbioscience.com (Peter Rice) Date: Wed, 28 Aug 2002 13:20:21 +0100 Subject: ACD not always required parameters References: <200208281156.NAA0001307743@blackjack.ben.vub.ac.be> Message-ID: <3D6CC005.3060705@uk.lionbioscience.com> gbottu at ben.vub.ac.be wrote: > Remains the problem of the required parameters. I send an > example as attachment. The data type is seqall. This will need a value. No value (empty default) means it tries to read nothing. It is a seqall (or sequence or seqset) that needs a value, the 'required' part is not important ... except of course if it is 'required' the user will be prompted. > You will note that the fields "userdb" and "userfastadb" have no reasonable > default. The one I had to add is an awfull hack. But delete default and run > "acdc fasta", you will get an error. The big problem here is trying to fit all the FASTA programs into one ACD file, instead of using 9 files. I did consider some time back extending ACD syntax to cover launching external applications with an ACD interface. There is an outline syntax definition including additional validation for (for example) blast gap penalties. The tricky part is testing the input is valid where it is a strange database (blast for example) before launching the application. Can anyone help with defining requirements for blast/fasta/etc. regards, Peter -- ------------------------------------------------ Peter Rice, LION Bioscience Ltd, Cambridge, UK peter.rice at uk.lionbioscience.com +44 1223 224723 From gwilliam at hgmp.mrc.ac.uk Wed Aug 28 14:43:47 2002 From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522) Date: Wed, 28 Aug 2002 15:43:47 +0100 Subject: automatic documentation from qatest data Message-ID: <3D6CE1A3.7B34@hgmp.mrc.ac.uk> I think I've got a workable system for automatically producing documentation of an application's Usage, Input files and Output files sections. The data for these sections is derived from the qatest.dat file. For examples, see: http://www.hgmp.mrc.ac.uk/Software/EMBOSS/Apps/antigenic.html http://www.hgmp.mrc.ac.uk/Software/EMBOSS/Apps/backtranseq.html http://www.hgmp.mrc.ac.uk/Software/EMBOSS/Apps/plotorf.html Comments please. Do the output gif files look OK you you in the plotorf documentation? Thanks, Gary -- 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 gbottu at ben.vub.ac.be Thu Aug 29 13:21:58 2002 From: gbottu at ben.vub.ac.be (gbottu at ben.vub.ac.be) Date: Thu, 29 Aug 2002 15:21:58 +0200 (CEST) Subject: fasta and ACD not always required parameters Message-ID: <200208291321.PAA0001348869@blackjack.vub.ac.be> > The data type is seqall. This will need a value. No value (empty default) > means it tries to read nothing. > > It is a seqall (or sequence or seqset) that needs a value, the 'required' > part is not important ... except of course if it is 'required' the user > will be prompted. Yes, you're right. The parameter "required" has nothing to do with it. The problem is that there are cases when where you sometimes need to read in a sequence and sometimes not, depending on the circumstances, and that there is obviously no good default here. The parameter "nullok" works for "infile" and "outfile". Maybe a good idea is to make "nullok" (or "missing" or whatever) work for any data type. > The big problem here is trying to fit all the FASTA programs into one ACD file, > instead of using 9 files. > > I did consider some time back extending ACD syntax to cover launching > external applications with an ACD interface. There is an outline syntax > definition including additional validation for (for example) blast gap > penalties. The tricky part is testing the input is valid where it is a > strange database (blast for example) before launching the application. > > Can anyone help with defining requirements for blast/fasta/etc. Making all fastA or BLAST options work in one rather than in 9 resp. 5 is not a problem, since I did it well. The problem is with the input of the search set. Since I did not try to "embossify" the original program but only wrote a wrapper application in EMBOSS, I had to consider 3 cases : 1) standard search set : the program uses an existing databank installed by BEN (in some cases a fastA "library" file or a BLAST .nal/.pal file is used) 2) user defined search set : the wrapper reads in a "seqall" and generates in /tmp a temporary databank in fastA or BLAST format. This could in principle be used always, but you understand we wouldn't like to do it for embl:* 3) user provided databank in fastA or BLAST format : used directly by the program. The wrapper does some testing before launching the program. For fastA the databank is read in as ftp::xxx and then typed with ajSeqTypeNuc/ajSeqTypeProt, for BLAST very crudely just the existence of three files with appropriate extension is tested. I admit that all this is tinkering rather than an elegant solution. For an in depth solution the programs themselves should be changed and/or several new features added to EMBOSS. In the meantime, just extending the "nullok" parameter to all data types should make me happy. Sincerely, Guy Bottu