From P.Ernst at dkfz-heidelberg.de Wed Jun 4 12:43:35 2003 From: P.Ernst at dkfz-heidelberg.de (Peter Ernst) Date: Wed, 4 Jun 2003 18:43:35 +0200 (MEST) Subject: extractfeat.acd: strange quoting Message-ID: Hi emboss-dev, a help string in extractfeat.acd is using un-escaped quotes ("). (parameter -decode) help: "To aid you .... '/gene="BRCA1"' associated .... label" ^^^ ^^^ It seems, that EMBOSS can somehow handle this. Also "acdvalid" doesn't complain. Concerning strings in ACD, now I have the following two questions: 1.) How EMBOSS detects the end of a quoted string ? 2.) Is this a valid acd string or not ? And a general question: 3.) Wouldn't it be nice to have beta releases before final releases? I didn't know how close we are to a release date and therefore I also didn't know, that I have to check W2H for compliance with 2.7.0. Now I found two problems in W2H ... I guess these problems could have been solved before a release .... (sorry I can not monitor the CVS version all the time). Kind regards, Peter -- ======================================================================= Peter Ernst Department of Molecular Biophysics - B020 Deutsches Krebsforschungszentrum (German Cancer Research Center) DKFZ Im Neuenheimer Feld 580 / Technologiepark 3 69120 Heidelberg, Germany phone: +49-6221-42-2330 http://genome.dkfz-heidelberg.de/ fax: +49-6221-42-2333 ======================================================================= From pmr at ebi.ac.uk Wed Jun 4 12:51:02 2003 From: pmr at ebi.ac.uk (Peter Rice) Date: Wed, 04 Jun 2003 17:51:02 +0100 Subject: extractfeat.acd: strange quoting References: Message-ID: <3EDE2376.6030506@ebi.ac.uk> Peter Ernst wrote: > a help string in extractfeat.acd is using un-escaped quotes ("). > (parameter -decode) > > help: "To aid you .... '/gene="BRCA1"' associated .... label" > ^^^ ^^^ > > It seems, that EMBOSS can somehow handle this. Also "acdvalid" doesn't > complain. > > Concerning strings in ACD, now I have the following two questions: > > 1.) How EMBOSS detects the end of a quoted string ? A quote at the end of a word. The "' stops EMBOSS finding this one. > 2.) Is this a valid acd string or not ? No. I will add a test for internal quotes - to all ACD processing. > And a general question: > > 3.) Wouldn't it be nice to have beta releases before final releases? We usually test and release, but an interim beta could be useful sometimes - especially for GUI developers of course. > I didn't know how close we are to a release date and therefore I > also didn't know, that I have to check W2H for compliance with > 2.7.0. Let us know what other problems you have - especially anything we can trap in acdvalid to make your life easier. regards, Peter Rice From asmann.Yan at mayo.edu Thu Jun 5 09:58:00 2003 From: asmann.Yan at mayo.edu (Asmann, Yan Ph.D.) Date: Thu, 5 Jun 2003 08:58:00 -0500 Subject: No subject Message-ID: Hi, I have installed the EMBOSS2.7.0, and tried to index databases using dbifasta. I found that when database size is over 2GB (e.g. est_human... etc), dbifasta will give EMBOSS An error message as following: " in embdbi.c at line 295: Cannot open ./est_mouse for reading" I remember for version 2.2.0, there wasn't any error message for over-sized DBs, the dbifasta would start indexing but an "fragmentation fault" will happen later. Has anyone had the same problem for 2.7.0? Is anyone working on modifying dbi* programes for DBs larger than 2GB? Thanks, Yan From ableasby at hgmp.mrc.ac.uk Thu Jun 5 10:14:14 2003 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Thu, 5 Jun 2003 15:14:14 +0100 (BST) Subject: Message-ID: <200306051414.h55EEEq07735@bromine.hgmp.mrc.ac.uk> Yes indeed, a rather flexible indexing system is being worked upon, only one of the requirements of which is the ability to index over 2Gb. Alan Bleasby HGMP From gbottu at ben.vub.ac.be Tue Jun 10 10:51:14 2003 From: gbottu at ben.vub.ac.be (Guy Bottu) Date: Tue, 10 Jun 2003 16:51:14 +0200 (CEST) Subject: problem with List Files + SRS access Message-ID: <200306101451.h5AEpE0k1310952@black.vub.ac.be> from : BEN Dear support, I just hit on a problem. I have an EMBOSS List File with more than 1000 entries that I try to give as input to an EMBOSS program. The program crashes with error message : task_create() failed for pid 1307576: max_proc_per_user (=256) exceeded for uid 430. EMBOSS An error in ajfile.c at line 125: fork create failed While the program is running, the command "ps x" gives : ... 1307703 pts/2 <+ 0:00.00 1307706 pts/2 <+ 0:00.00 1307713 pts/2 <+ 0:00.00 1307714 pts/2 R + 0:00.29 getz -e [EMBL-id:AF017184]|[EMBL-acc:AF017184] 1307720 pts/2 <+ 0:00.00 1307722 pts/2 <+ 0:00.00 1307729 pts/2 <+ 0:00.00 ... Note that the EMBL databank is accessed by the "srs" method. For databanks acessed by the "emblcd" method there is no problem. Looks like a bug in the interface between EMBOSS and "getz", doesn'it ? (I am using EMBOSS 2.6.0 under CompaqTru64 5.1A). Sincerely, Guy Bottu From raouljp at libero.it Thu Jun 26 05:56:01 2003 From: raouljp at libero.it (=?iso-8859-1?Q?raouljp?=) Date: Thu, 26 Jun 2003 11:56:01 +0200 Subject: =?iso-8859-1?Q?ajListSort_problem.?= Message-ID: hi all, i have had various problem to understand how it work. Documentation is undocumented about specification of "compare" 's function. void ajListSort (AjPList thys, int (*compar) (const void*, const void*)); const void* is a pointer to pointer so, an example of comapre function is, in emboss style : static ajint myCompare(const void* x, const void* y) { MyPItemListType *item_one = NULL; MyPItemListType *item_second = NULL; item_one = ( MyPItemType* ) x; item_second = ( MyPItemType*) y; then your criteria accessing : *item_one, *item_second return an int value; } If i have mis understood something plez you explain to me. by R.J.P.B. From P.Ernst at dkfz-heidelberg.de Wed Jun 4 16:43:35 2003 From: P.Ernst at dkfz-heidelberg.de (Peter Ernst) Date: Wed, 4 Jun 2003 18:43:35 +0200 (MEST) Subject: extractfeat.acd: strange quoting Message-ID: Hi emboss-dev, a help string in extractfeat.acd is using un-escaped quotes ("). (parameter -decode) help: "To aid you .... '/gene="BRCA1"' associated .... label" ^^^ ^^^ It seems, that EMBOSS can somehow handle this. Also "acdvalid" doesn't complain. Concerning strings in ACD, now I have the following two questions: 1.) How EMBOSS detects the end of a quoted string ? 2.) Is this a valid acd string or not ? And a general question: 3.) Wouldn't it be nice to have beta releases before final releases? I didn't know how close we are to a release date and therefore I also didn't know, that I have to check W2H for compliance with 2.7.0. Now I found two problems in W2H ... I guess these problems could have been solved before a release .... (sorry I can not monitor the CVS version all the time). Kind regards, Peter -- ======================================================================= Peter Ernst Department of Molecular Biophysics - B020 Deutsches Krebsforschungszentrum (German Cancer Research Center) DKFZ Im Neuenheimer Feld 580 / Technologiepark 3 69120 Heidelberg, Germany phone: +49-6221-42-2330 http://genome.dkfz-heidelberg.de/ fax: +49-6221-42-2333 ======================================================================= From pmr at ebi.ac.uk Wed Jun 4 16:51:02 2003 From: pmr at ebi.ac.uk (Peter Rice) Date: Wed, 04 Jun 2003 17:51:02 +0100 Subject: extractfeat.acd: strange quoting References: Message-ID: <3EDE2376.6030506@ebi.ac.uk> Peter Ernst wrote: > a help string in extractfeat.acd is using un-escaped quotes ("). > (parameter -decode) > > help: "To aid you .... '/gene="BRCA1"' associated .... label" > ^^^ ^^^ > > It seems, that EMBOSS can somehow handle this. Also "acdvalid" doesn't > complain. > > Concerning strings in ACD, now I have the following two questions: > > 1.) How EMBOSS detects the end of a quoted string ? A quote at the end of a word. The "' stops EMBOSS finding this one. > 2.) Is this a valid acd string or not ? No. I will add a test for internal quotes - to all ACD processing. > And a general question: > > 3.) Wouldn't it be nice to have beta releases before final releases? We usually test and release, but an interim beta could be useful sometimes - especially for GUI developers of course. > I didn't know how close we are to a release date and therefore I > also didn't know, that I have to check W2H for compliance with > 2.7.0. Let us know what other problems you have - especially anything we can trap in acdvalid to make your life easier. regards, Peter Rice From asmann.Yan at mayo.edu Thu Jun 5 13:58:00 2003 From: asmann.Yan at mayo.edu (Asmann, Yan Ph.D.) Date: Thu, 5 Jun 2003 08:58:00 -0500 Subject: No subject Message-ID: Hi, I have installed the EMBOSS2.7.0, and tried to index databases using dbifasta. I found that when database size is over 2GB (e.g. est_human... etc), dbifasta will give EMBOSS An error message as following: " in embdbi.c at line 295: Cannot open ./est_mouse for reading" I remember for version 2.2.0, there wasn't any error message for over-sized DBs, the dbifasta would start indexing but an "fragmentation fault" will happen later. Has anyone had the same problem for 2.7.0? Is anyone working on modifying dbi* programes for DBs larger than 2GB? Thanks, Yan From ableasby at hgmp.mrc.ac.uk Thu Jun 5 14:14:14 2003 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Thu, 5 Jun 2003 15:14:14 +0100 (BST) Subject: Message-ID: <200306051414.h55EEEq07735@bromine.hgmp.mrc.ac.uk> Yes indeed, a rather flexible indexing system is being worked upon, only one of the requirements of which is the ability to index over 2Gb. Alan Bleasby HGMP From gbottu at ben.vub.ac.be Tue Jun 10 14:51:14 2003 From: gbottu at ben.vub.ac.be (Guy Bottu) Date: Tue, 10 Jun 2003 16:51:14 +0200 (CEST) Subject: problem with List Files + SRS access Message-ID: <200306101451.h5AEpE0k1310952@black.vub.ac.be> from : BEN Dear support, I just hit on a problem. I have an EMBOSS List File with more than 1000 entries that I try to give as input to an EMBOSS program. The program crashes with error message : task_create() failed for pid 1307576: max_proc_per_user (=256) exceeded for uid 430. EMBOSS An error in ajfile.c at line 125: fork create failed While the program is running, the command "ps x" gives : ... 1307703 pts/2 <+ 0:00.00 1307706 pts/2 <+ 0:00.00 1307713 pts/2 <+ 0:00.00 1307714 pts/2 R + 0:00.29 getz -e [EMBL-id:AF017184]|[EMBL-acc:AF017184] 1307720 pts/2 <+ 0:00.00 1307722 pts/2 <+ 0:00.00 1307729 pts/2 <+ 0:00.00 ... Note that the EMBL databank is accessed by the "srs" method. For databanks acessed by the "emblcd" method there is no problem. Looks like a bug in the interface between EMBOSS and "getz", doesn'it ? (I am using EMBOSS 2.6.0 under CompaqTru64 5.1A). Sincerely, Guy Bottu From raouljp at libero.it Thu Jun 26 09:56:01 2003 From: raouljp at libero.it (=?iso-8859-1?Q?raouljp?=) Date: Thu, 26 Jun 2003 11:56:01 +0200 Subject: =?iso-8859-1?Q?ajListSort_problem.?= Message-ID: hi all, i have had various problem to understand how it work. Documentation is undocumented about specification of "compare" 's function. void ajListSort (AjPList thys, int (*compar) (const void*, const void*)); const void* is a pointer to pointer so, an example of comapre function is, in emboss style : static ajint myCompare(const void* x, const void* y) { MyPItemListType *item_one = NULL; MyPItemListType *item_second = NULL; item_one = ( MyPItemType* ) x; item_second = ( MyPItemType*) y; then your criteria accessing : *item_one, *item_second return an int value; } If i have mis understood something plez you explain to me. by R.J.P.B.