From wshui at cse.unsw.edu.au Wed Aug 1 12:48:15 2001 From: wshui at cse.unsw.edu.au (Bill Shui) Date: Wed, 1 Aug 2001 16:48:15 +0000 Subject: Question on Edatas Message-ID: <20010801164815.A5750@nimky.cse.unsw.edu.au> Hi all, I'm using EMBOSS as part of my honours project at the moment. I'm in the process of disecting the entire emboss package and use only some of the ajax and nucleus libraries. However, I was just wandering as to the data files that were packaged with the release. Are they example data files or are they being used by one of the emboss programs? I know that the file "Edayhoff.freq" is being used by pepstat so I assume that all of these data files are being used by other programs rather than just being example data files. Am I right on this? Please advice. thanks in advance. Bill -- There are three kinds of people: men, women, and unix. ------------------------------------------------------ Bill Shui Email: wshui at cse.unsw.edu.au From ableasby at hgmp.mrc.ac.uk Wed Aug 1 02:53:31 2001 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Wed, 1 Aug 2001 07:53:31 +0100 (BST) Subject: Question on Edatas Message-ID: <200108010653.HAA05098@bromine.hgmp.mrc.ac.uk> Hi, The files in the embdoss/data directory and subdirectories contain data that is essential to the operation of either applications or indeed to the library (e.g. the Efeatures data for feature tables). The data in test/data are generally for quality testing or examples. HTH Alan From touro at capoeirabrasil.com.au Mon Aug 6 11:03:07 2001 From: touro at capoeirabrasil.com.au (Bill Shui) Date: Tue, 7 Aug 2001 01:03:07 +1000 Subject: interpreting ajtranslate.* in ajax library. Message-ID: <20010807010307.A17321@capoeira.sydney> Hi there, I'm using EMBOSS as part of my honours thesis. What I am doing now is breaking up all the library modules and reuse bits of them to get something working. However, I am stuck with ajtranslate or the transeq program. In the file ajtranslate.c, the function ajTrnReadFile uses struct AjSTrn to store the EGC data (well at least that's how I understood it) correct me if I was wrong. Now, I don't understand why the variable GC and Starts in AjSTrn are 15 by 15 by 15 matrices? I also do not understand the meaning of initialisation of the char arrays trnconv and trncomp. and why most of the arrays are 14? your prompt reply to this is much appreciated as I really need this for my thesis and I'm on a tight schedule. thanks in advance. regards. Bill -- The mark of a good party is that you wake up the next morning wanting to change your name and start a new life in different city. -- Vance Bourjaily, "Esquire" --------------------------------------------- Bill Shui Email: wshui at bigpond.net.au wshui at cse.unsw.edu.au touro at capoeirabrasil.com.au bill.shui at proteomesystems.com Bioinformatics Programmer From gwilliam at hgmp.mrc.ac.uk Mon Aug 6 11:24:13 2001 From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522) Date: Mon, 06 Aug 2001 16:24:13 +0100 Subject: interpreting ajtranslate.* in ajax library. References: <20010807010307.A17321@capoeira.sydney> Message-ID: <3B6EB69C.FFD741C8@hgmp.mrc.ac.uk> Bill Shui wrote: > > Hi there, > I'm using EMBOSS as part of my honours thesis. What I am doing now is > breaking up all the library modules and reuse bits of them to get something > working. > > However, I am stuck with ajtranslate or the transeq program. > > In the file ajtranslate.c, the function ajTrnReadFile uses struct > AjSTrn to store the EGC data (well at least that's how I understood it) > correct me if I was wrong. Correct. > Now, I don't understand why the variable GC and Starts in > AjSTrn are 15 by 15 by 15 matrices? Each codon has 3 bases, so we use a 3-dimensional array to convert the codons to residues. The size of the array could be 4x4x4 for most purposes (there are four bases: A, C, G, T) but sometimes ambiguity codes are used in positions where the base is uncertain, e.g. 'M' codes for 'A' or 'C'. There are 15 bases if you include these ambiguity codes (including 'N' for the completely unknown base). So to translate codons that have ambiguity codes in them, you really need a 15x15x15 matrix. Similarly, for the Start codons, although there are far fewer codons that are Start codons and so this could probably have been done in a more memory efficient way. > I also do not understand the meaning of initialisation of > the char arrays trnconv and trncomp. To look up an element in the 15x15x15 codon to residue matrix, you need to convert the bases to numbers. This is what trnconv[] is for. trncomp[] does the same thing, but gives you the number of the code for the complement - this is used for translating the complement of the sequence. > and why most of the arrays are 14? Most of the arrays trnconv[] and trncomp[] hold '14' because this is the code I am using for 'N' (unknown) - these are letters that do not correspond to any recognised nucleotide code letter (i.e. they are not one of: ACGTUMRWSYKVHDBN). See: http://www.chem.qmw.ac.uk/iupac/misc/naseq.html for details of the ambiguity codes. > your prompt reply to this is much appreciated as I really need this for my > thesis and I'm on a tight schedule. Is this soon enough for you? > thanks in advance. > > regards. > > Bill > -- > The mark of a good party is that you wake up the next morning > wanting to change your name and start a new life in different > city. > -- Vance Bourjaily, "Esquire" > --------------------------------------------- > Bill Shui Email: wshui at bigpond.net.au > wshui at cse.unsw.edu.au > touro at capoeirabrasil.com.au > bill.shui at proteomesystems.com > Bioinformatics Programmer -- 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 dmartin at bioinformatics.msiwtb.dundee.ac.uk Wed Aug 8 11:23:25 2001 From: dmartin at bioinformatics.msiwtb.dundee.ac.uk (David Martin) Date: Wed, 8 Aug 2001 16:23:25 +0100 (BST) Subject: Using the dynamic arrays in a random access manner Message-ID: One problem with using the 2d and higher arrays in ajarr.c is that if one doesn't fill them sequentially but instead uses them in a semi sparse manner this can lead to problems. If one wants the size of an array teh current function calls return the maximum dimensions, but this doesn't neccessarily mean that every point within that area has been allocated. This can lead to a warning or worse when trying to aj...Get the value and the particular one dimensional array doesn't stretch that far or hasn't been allocated at all. I have a couple of patches for the Int2d arrays which add two more function calls ajInt2dLenElem (gets the second dimension length at any particular specified first dimension position) and ajInt2dElemExists which checks to see whether an element has indeed been allocated yet. The alternative is to roll some of this into ajInt2dGet so that an attempt to access an unallocated element returns null or zero instead of throwing an error, but I am not sure that is completely desirable. Thoughts ..d ---------------------------------- David Martin PhD Bioinformatics Scientific Officer Wellcome Trust Biocentre, Dundee ---------------------------------- From ableasby at hgmp.mrc.ac.uk Wed Aug 8 13:25:54 2001 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Wed, 8 Aug 2001 18:25:54 +0100 (BST) Subject: Using the dynamic arrays in a random access manner Message-ID: <200108081725.SAA11200@bromine.hgmp.mrc.ac.uk> The proposed functions certainly wouldn't hurt anything but their use would really be a programming style matter. Cheers Alan From gbottu at ben.vub.ac.be Wed Aug 15 12:11:41 2001 From: gbottu at ben.vub.ac.be (Guy Bottu) Date: Wed, 15 Aug 2001 18:11:41 +0200 (MET DST) Subject: EMBOSS whish list Message-ID: <200108151611.SAA13664@bigben.vub.ac.be> from : BEN Dear colleagues, I know it is easy to say "we need this, we need that !", while it takes so much time and effort to program. Nevertheless, I take the liberty to make a few suggestions for improvements that would help EMBOSS to equal and even surpass GCG in userfriendliness : - for graphic display : an X-Window graphic with "zoom" function, also tektronix emulation in color. - a mechanism to easily submit programs to a "batch queue" from the command line (comparable to the -batch parameter of GCG and egcg) - at the present it is difficult to find out which data file(s) a program uses and hence to put an alternative data file in the working directory. You have to read exhaustively the on-line manual. It would be nice if there was always a command line parameter with default value that would appear if you do xxx -help or alternatively maybe a new General Parameter to make e.g. xxx -datafile to make a program display its data file names. The data file name should preferable appear in the ACD file so that the parsers that generate pages for the graphical user interfaces can find it. - the possibility to input/output sequences from any program in any format should be extended to other kinds of data. E.g. base/aa symbol comparison tables : GCG, BLAST, SIM,... codon usage tables : GCG, CUTG,... 3D structures : PDB, Kinemage,... (is already being done ?) ... Sincerely, Guy Bottu From jkb at mrc-lmb.cam.ac.uk Wed Aug 15 12:22:44 2001 From: jkb at mrc-lmb.cam.ac.uk (James Bonfield) Date: Wed, 15 Aug 2001 17:22:44 +0100 Subject: EMBOSS whish list In-Reply-To: <200108151611.SAA13664@bigben.vub.ac.be>; from gbottu@ben.vub.ac.be on Wed, Aug 15, 2001 at 06:11:41PM +0200 References: <200108151611.SAA13664@bigben.vub.ac.be> Message-ID: <20010815172244.B30470@arran.mrc-lmb.cam.ac.uk> On Wed, Aug 15, 2001 at 06:11:41PM +0200, Guy Bottu wrote: > - for graphic display : an X-Window graphic with "zoom" function, also tektronix > emulation in color. Maybe now is the time for a quick plug (sorry). We've (finally) managed to make an official release of "spin". This includes a graphical interface to EMBOSS, including the ability to zoom, scroll and superimpose plots. Spin is still in its early days as an EMBOSS interface (although it has its own algorithms too, some of which date back to before the dawn of time). See http://www.mrc-lmb.cam.ac.uk/pubseq/ for more details. Alas it doesn't solve your other problems. I've also heard via the grapevine that another graphical interface to EMBOSS is in development; using Java. Is there any news on the progress of this? > e.g. xxx -datafile > to make a program display its data file names. The data file name should > preferable appear in the ACD file so that the parsers that generate pages for > the graphical user interfaces can find it. This is a good point. We found this horrid to do, especially for the programs that generate an arbitrary number of output files. Before running the programs we delete all {progname}.dat[0-9]* files. Then after running we do a filename 'glob' to see which files have been created. This works OK, but can really catch out the user if they try to have an input file named "syco.dat" (for example)! James -- James Bonfield (jkb at mrc-lmb.cam.ac.uk) Tel: 01223 402499 Fax: 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 ableasby at hgmp.mrc.ac.uk Wed Aug 15 16:04:50 2001 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Wed, 15 Aug 2001 21:04:50 +0100 (BST) Subject: EMBOSS whish list Message-ID: <200108152004.VAA14659@bromine.hgmp.mrc.ac.uk> The java interface (currently called jEMBOSS) is still under development and hopefully will be released before the end of the year. It doesn't have anything as fancy as zoom yet. Maybe the title should have been swish list? We have filled one of the programming posts (corba and soapy things) and are hoping to fill the other soon. The intention is for the second post to work in the graphics area (openGL etc). Alan PS: Other points noted. From brooks at embl-grenoble.fr Mon Aug 20 12:54:02 2001 From: brooks at embl-grenoble.fr (Brooks Mark) Date: Mon, 20 Aug 2001 18:54:02 +0200 Subject: Using the ajSeqRead function.... References: <200108081725.SAA11200@bromine.hgmp.mrc.ac.uk> Message-ID: <3B8140A9.4FF833AE@embl-grenoble.fr> Hi all, I have run into a bit of a problem when trying to open a file from a file selection dialog. I need to parse (nucleotide) sequence files and spit their contents into AjPSeq instances. Question 1: Am I right in thinking that ajSeqRead should parse these files in this manner? If so: Question 2: Am I doing this right? Here is a simplified code snippet: ------------->8-------------------8<------------------ int open_ok () { AjPSeq seq; AjPSeqin seqIn; AjPStr seqfileInName; seq = ajSeqNew (); seqIn = ajSeqinNew (); seqfileInName = ajStrNewC("actin.seq"); ajSeqinUsa ( &seqIn , seqfileInName ); ajSeqinSetNuc (seqIn); ajSeqRead (seq , seqIn); ajSeqinDel (&seqIn); return 0; } ------------->8-------------------8<------------------ Sorry if it's a daft pair of questions, I'm a bit of a newbie! (Hence my poor code too!) Thanks in advance for any comments, Mark -- Mark Brooks, EMBL Grenoble Outstation, 6, rue Jules Horowitz, BP181 38042 Grenoble Cedex 9, France. Tel: + (0)4 76 20 72 85 From ableasby at hgmp.mrc.ac.uk Mon Aug 20 15:06:53 2001 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Mon, 20 Aug 2001 20:06:53 +0100 (BST) Subject: Using the ajSeqRead function.... Message-ID: <200108201906.UAA26210@bromine.hgmp.mrc.ac.uk> Hi Mark, There is a functio already for doing that sort of thing i.e. ajSeqGetFromUsa Give it a USA and say whether the sequence is a protein or not. It'll return a filled AjPSeq. HTH Alan From dmartin at bioinformatics.msiwtb.dundee.ac.uk Wed Aug 22 11:30:42 2001 From: dmartin at bioinformatics.msiwtb.dundee.ac.uk (David Martin) Date: Wed, 22 Aug 2001 16:30:42 +0100 (BST) Subject: USA extensions Message-ID: A long time ago on the wish list it was mooted that USA's could be extended to include region information. Has anything come of this and what are the thoughts on feasibility. In other words it would be nice to be able to write a listfile like em:hstf[30..90] em:hscfvii[92..103,108-120] ..d ---------------------------------- David Martin PhD Bioinformatics Scientific Officer Wellcome Trust Biocentre, Dundee ---------------------------------- From peter.rice at uk.lionbioscience.com Wed Aug 22 11:34:01 2001 From: peter.rice at uk.lionbioscience.com (Peter Rice) Date: Wed, 22 Aug 2001 16:34:01 +0100 Subject: USA extensions References: Message-ID: <3B83D0E9.248C58D0@uk.lionbioscience.com> David Martin wrote: > > A long time ago on the wish list it was mooted that USA's could be > extended to include region information. Has anything come of this and what > are the thoughts on feasibility. > > In other words it would be nice to be able to write a listfile like > > em:hstf[30..90] > em:hscfvii[92..103,108-120] Something to discuss at this week's EMBOSS meeting.... Among the possible 'report' formats for writing 'feature' data (any program that reports start, end and score for some pattern) is a ListFile format to write a list file that can be used to read in the subsequences. For this we do need a USA syntax that includes start, end, reverse. The syntax above would be a reasonable solution (with to..from for reversed sequences) Peter -- ------------------------------------------------ Peter Rice, LION Bioscience Ltd, Cambridge, UK peter.rice at uk.lionbioscience.com +44 1223 224723 From wshui at cse.unsw.edu.au Wed Aug 1 16:48:15 2001 From: wshui at cse.unsw.edu.au (Bill Shui) Date: Wed, 1 Aug 2001 16:48:15 +0000 Subject: Question on Edatas Message-ID: <20010801164815.A5750@nimky.cse.unsw.edu.au> Hi all, I'm using EMBOSS as part of my honours project at the moment. I'm in the process of disecting the entire emboss package and use only some of the ajax and nucleus libraries. However, I was just wandering as to the data files that were packaged with the release. Are they example data files or are they being used by one of the emboss programs? I know that the file "Edayhoff.freq" is being used by pepstat so I assume that all of these data files are being used by other programs rather than just being example data files. Am I right on this? Please advice. thanks in advance. Bill -- There are three kinds of people: men, women, and unix. ------------------------------------------------------ Bill Shui Email: wshui at cse.unsw.edu.au From ableasby at hgmp.mrc.ac.uk Wed Aug 1 06:53:31 2001 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Wed, 1 Aug 2001 07:53:31 +0100 (BST) Subject: Question on Edatas Message-ID: <200108010653.HAA05098@bromine.hgmp.mrc.ac.uk> Hi, The files in the embdoss/data directory and subdirectories contain data that is essential to the operation of either applications or indeed to the library (e.g. the Efeatures data for feature tables). The data in test/data are generally for quality testing or examples. HTH Alan From touro at capoeirabrasil.com.au Mon Aug 6 15:03:07 2001 From: touro at capoeirabrasil.com.au (Bill Shui) Date: Tue, 7 Aug 2001 01:03:07 +1000 Subject: interpreting ajtranslate.* in ajax library. Message-ID: <20010807010307.A17321@capoeira.sydney> Hi there, I'm using EMBOSS as part of my honours thesis. What I am doing now is breaking up all the library modules and reuse bits of them to get something working. However, I am stuck with ajtranslate or the transeq program. In the file ajtranslate.c, the function ajTrnReadFile uses struct AjSTrn to store the EGC data (well at least that's how I understood it) correct me if I was wrong. Now, I don't understand why the variable GC and Starts in AjSTrn are 15 by 15 by 15 matrices? I also do not understand the meaning of initialisation of the char arrays trnconv and trncomp. and why most of the arrays are 14? your prompt reply to this is much appreciated as I really need this for my thesis and I'm on a tight schedule. thanks in advance. regards. Bill -- The mark of a good party is that you wake up the next morning wanting to change your name and start a new life in different city. -- Vance Bourjaily, "Esquire" --------------------------------------------- Bill Shui Email: wshui at bigpond.net.au wshui at cse.unsw.edu.au touro at capoeirabrasil.com.au bill.shui at proteomesystems.com Bioinformatics Programmer From gwilliam at hgmp.mrc.ac.uk Mon Aug 6 15:24:13 2001 From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522) Date: Mon, 06 Aug 2001 16:24:13 +0100 Subject: interpreting ajtranslate.* in ajax library. References: <20010807010307.A17321@capoeira.sydney> Message-ID: <3B6EB69C.FFD741C8@hgmp.mrc.ac.uk> Bill Shui wrote: > > Hi there, > I'm using EMBOSS as part of my honours thesis. What I am doing now is > breaking up all the library modules and reuse bits of them to get something > working. > > However, I am stuck with ajtranslate or the transeq program. > > In the file ajtranslate.c, the function ajTrnReadFile uses struct > AjSTrn to store the EGC data (well at least that's how I understood it) > correct me if I was wrong. Correct. > Now, I don't understand why the variable GC and Starts in > AjSTrn are 15 by 15 by 15 matrices? Each codon has 3 bases, so we use a 3-dimensional array to convert the codons to residues. The size of the array could be 4x4x4 for most purposes (there are four bases: A, C, G, T) but sometimes ambiguity codes are used in positions where the base is uncertain, e.g. 'M' codes for 'A' or 'C'. There are 15 bases if you include these ambiguity codes (including 'N' for the completely unknown base). So to translate codons that have ambiguity codes in them, you really need a 15x15x15 matrix. Similarly, for the Start codons, although there are far fewer codons that are Start codons and so this could probably have been done in a more memory efficient way. > I also do not understand the meaning of initialisation of > the char arrays trnconv and trncomp. To look up an element in the 15x15x15 codon to residue matrix, you need to convert the bases to numbers. This is what trnconv[] is for. trncomp[] does the same thing, but gives you the number of the code for the complement - this is used for translating the complement of the sequence. > and why most of the arrays are 14? Most of the arrays trnconv[] and trncomp[] hold '14' because this is the code I am using for 'N' (unknown) - these are letters that do not correspond to any recognised nucleotide code letter (i.e. they are not one of: ACGTUMRWSYKVHDBN). See: http://www.chem.qmw.ac.uk/iupac/misc/naseq.html for details of the ambiguity codes. > your prompt reply to this is much appreciated as I really need this for my > thesis and I'm on a tight schedule. Is this soon enough for you? > thanks in advance. > > regards. > > Bill > -- > The mark of a good party is that you wake up the next morning > wanting to change your name and start a new life in different > city. > -- Vance Bourjaily, "Esquire" > --------------------------------------------- > Bill Shui Email: wshui at bigpond.net.au > wshui at cse.unsw.edu.au > touro at capoeirabrasil.com.au > bill.shui at proteomesystems.com > Bioinformatics Programmer -- 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 dmartin at bioinformatics.msiwtb.dundee.ac.uk Wed Aug 8 15:23:25 2001 From: dmartin at bioinformatics.msiwtb.dundee.ac.uk (David Martin) Date: Wed, 8 Aug 2001 16:23:25 +0100 (BST) Subject: Using the dynamic arrays in a random access manner Message-ID: One problem with using the 2d and higher arrays in ajarr.c is that if one doesn't fill them sequentially but instead uses them in a semi sparse manner this can lead to problems. If one wants the size of an array teh current function calls return the maximum dimensions, but this doesn't neccessarily mean that every point within that area has been allocated. This can lead to a warning or worse when trying to aj...Get the value and the particular one dimensional array doesn't stretch that far or hasn't been allocated at all. I have a couple of patches for the Int2d arrays which add two more function calls ajInt2dLenElem (gets the second dimension length at any particular specified first dimension position) and ajInt2dElemExists which checks to see whether an element has indeed been allocated yet. The alternative is to roll some of this into ajInt2dGet so that an attempt to access an unallocated element returns null or zero instead of throwing an error, but I am not sure that is completely desirable. Thoughts ..d ---------------------------------- David Martin PhD Bioinformatics Scientific Officer Wellcome Trust Biocentre, Dundee ---------------------------------- From ableasby at hgmp.mrc.ac.uk Wed Aug 8 17:25:54 2001 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Wed, 8 Aug 2001 18:25:54 +0100 (BST) Subject: Using the dynamic arrays in a random access manner Message-ID: <200108081725.SAA11200@bromine.hgmp.mrc.ac.uk> The proposed functions certainly wouldn't hurt anything but their use would really be a programming style matter. Cheers Alan From gbottu at ben.vub.ac.be Wed Aug 15 16:11:41 2001 From: gbottu at ben.vub.ac.be (Guy Bottu) Date: Wed, 15 Aug 2001 18:11:41 +0200 (MET DST) Subject: EMBOSS whish list Message-ID: <200108151611.SAA13664@bigben.vub.ac.be> from : BEN Dear colleagues, I know it is easy to say "we need this, we need that !", while it takes so much time and effort to program. Nevertheless, I take the liberty to make a few suggestions for improvements that would help EMBOSS to equal and even surpass GCG in userfriendliness : - for graphic display : an X-Window graphic with "zoom" function, also tektronix emulation in color. - a mechanism to easily submit programs to a "batch queue" from the command line (comparable to the -batch parameter of GCG and egcg) - at the present it is difficult to find out which data file(s) a program uses and hence to put an alternative data file in the working directory. You have to read exhaustively the on-line manual. It would be nice if there was always a command line parameter with default value that would appear if you do xxx -help or alternatively maybe a new General Parameter to make e.g. xxx -datafile to make a program display its data file names. The data file name should preferable appear in the ACD file so that the parsers that generate pages for the graphical user interfaces can find it. - the possibility to input/output sequences from any program in any format should be extended to other kinds of data. E.g. base/aa symbol comparison tables : GCG, BLAST, SIM,... codon usage tables : GCG, CUTG,... 3D structures : PDB, Kinemage,... (is already being done ?) ... Sincerely, Guy Bottu From jkb at mrc-lmb.cam.ac.uk Wed Aug 15 16:22:44 2001 From: jkb at mrc-lmb.cam.ac.uk (James Bonfield) Date: Wed, 15 Aug 2001 17:22:44 +0100 Subject: EMBOSS whish list In-Reply-To: <200108151611.SAA13664@bigben.vub.ac.be>; from gbottu@ben.vub.ac.be on Wed, Aug 15, 2001 at 06:11:41PM +0200 References: <200108151611.SAA13664@bigben.vub.ac.be> Message-ID: <20010815172244.B30470@arran.mrc-lmb.cam.ac.uk> On Wed, Aug 15, 2001 at 06:11:41PM +0200, Guy Bottu wrote: > - for graphic display : an X-Window graphic with "zoom" function, also tektronix > emulation in color. Maybe now is the time for a quick plug (sorry). We've (finally) managed to make an official release of "spin". This includes a graphical interface to EMBOSS, including the ability to zoom, scroll and superimpose plots. Spin is still in its early days as an EMBOSS interface (although it has its own algorithms too, some of which date back to before the dawn of time). See http://www.mrc-lmb.cam.ac.uk/pubseq/ for more details. Alas it doesn't solve your other problems. I've also heard via the grapevine that another graphical interface to EMBOSS is in development; using Java. Is there any news on the progress of this? > e.g. xxx -datafile > to make a program display its data file names. The data file name should > preferable appear in the ACD file so that the parsers that generate pages for > the graphical user interfaces can find it. This is a good point. We found this horrid to do, especially for the programs that generate an arbitrary number of output files. Before running the programs we delete all {progname}.dat[0-9]* files. Then after running we do a filename 'glob' to see which files have been created. This works OK, but can really catch out the user if they try to have an input file named "syco.dat" (for example)! James -- James Bonfield (jkb at mrc-lmb.cam.ac.uk) Tel: 01223 402499 Fax: 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 ableasby at hgmp.mrc.ac.uk Wed Aug 15 20:04:50 2001 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Wed, 15 Aug 2001 21:04:50 +0100 (BST) Subject: EMBOSS whish list Message-ID: <200108152004.VAA14659@bromine.hgmp.mrc.ac.uk> The java interface (currently called jEMBOSS) is still under development and hopefully will be released before the end of the year. It doesn't have anything as fancy as zoom yet. Maybe the title should have been swish list? We have filled one of the programming posts (corba and soapy things) and are hoping to fill the other soon. The intention is for the second post to work in the graphics area (openGL etc). Alan PS: Other points noted. From brooks at embl-grenoble.fr Mon Aug 20 16:54:02 2001 From: brooks at embl-grenoble.fr (Brooks Mark) Date: Mon, 20 Aug 2001 18:54:02 +0200 Subject: Using the ajSeqRead function.... References: <200108081725.SAA11200@bromine.hgmp.mrc.ac.uk> Message-ID: <3B8140A9.4FF833AE@embl-grenoble.fr> Hi all, I have run into a bit of a problem when trying to open a file from a file selection dialog. I need to parse (nucleotide) sequence files and spit their contents into AjPSeq instances. Question 1: Am I right in thinking that ajSeqRead should parse these files in this manner? If so: Question 2: Am I doing this right? Here is a simplified code snippet: ------------->8-------------------8<------------------ int open_ok () { AjPSeq seq; AjPSeqin seqIn; AjPStr seqfileInName; seq = ajSeqNew (); seqIn = ajSeqinNew (); seqfileInName = ajStrNewC("actin.seq"); ajSeqinUsa ( &seqIn , seqfileInName ); ajSeqinSetNuc (seqIn); ajSeqRead (seq , seqIn); ajSeqinDel (&seqIn); return 0; } ------------->8-------------------8<------------------ Sorry if it's a daft pair of questions, I'm a bit of a newbie! (Hence my poor code too!) Thanks in advance for any comments, Mark -- Mark Brooks, EMBL Grenoble Outstation, 6, rue Jules Horowitz, BP181 38042 Grenoble Cedex 9, France. Tel: + (0)4 76 20 72 85 From ableasby at hgmp.mrc.ac.uk Mon Aug 20 19:06:53 2001 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Mon, 20 Aug 2001 20:06:53 +0100 (BST) Subject: Using the ajSeqRead function.... Message-ID: <200108201906.UAA26210@bromine.hgmp.mrc.ac.uk> Hi Mark, There is a functio already for doing that sort of thing i.e. ajSeqGetFromUsa Give it a USA and say whether the sequence is a protein or not. It'll return a filled AjPSeq. HTH Alan From dmartin at bioinformatics.msiwtb.dundee.ac.uk Wed Aug 22 15:30:42 2001 From: dmartin at bioinformatics.msiwtb.dundee.ac.uk (David Martin) Date: Wed, 22 Aug 2001 16:30:42 +0100 (BST) Subject: USA extensions Message-ID: A long time ago on the wish list it was mooted that USA's could be extended to include region information. Has anything come of this and what are the thoughts on feasibility. In other words it would be nice to be able to write a listfile like em:hstf[30..90] em:hscfvii[92..103,108-120] ..d ---------------------------------- David Martin PhD Bioinformatics Scientific Officer Wellcome Trust Biocentre, Dundee ---------------------------------- From peter.rice at uk.lionbioscience.com Wed Aug 22 15:34:01 2001 From: peter.rice at uk.lionbioscience.com (Peter Rice) Date: Wed, 22 Aug 2001 16:34:01 +0100 Subject: USA extensions References: Message-ID: <3B83D0E9.248C58D0@uk.lionbioscience.com> David Martin wrote: > > A long time ago on the wish list it was mooted that USA's could be > extended to include region information. Has anything come of this and what > are the thoughts on feasibility. > > In other words it would be nice to be able to write a listfile like > > em:hstf[30..90] > em:hscfvii[92..103,108-120] Something to discuss at this week's EMBOSS meeting.... Among the possible 'report' formats for writing 'feature' data (any program that reports start, end and score for some pattern) is a ListFile format to write a list file that can be used to read in the subsequences. For this we do need a USA syntax that includes start, end, reverse. The syntax above would be a reasonable solution (with to..from for reversed sequences) Peter -- ------------------------------------------------ Peter Rice, LION Bioscience Ltd, Cambridge, UK peter.rice at uk.lionbioscience.com +44 1223 224723