From ableasby at hgmp.mrc.ac.uk Wed Jul 13 10:37:40 2005 From: ableasby at hgmp.mrc.ac.uk (Alan Bleasby) Date: Wed, 13 Jul 2005 15:37:40 +0100 (BST) Subject: [emboss-dev] New email lists ready Message-ID: <200507131437.j6DEbe8r027649@bromine.hgmp.mrc.ac.uk> The new email addresses for the EMBOSS lists are now set up and ready (excluding any teething problems). They are: emboss at emboss.open-bio.org emboss-dev at emboss.open-bio.org emboss-bug at emboss.open-bio.org emboss-submit at emboss.open-bio.org You can access the archives, subscribe/unsubscribe and alter the way email is sent to you (e.g. digests) by visiting: http://emboss.open-bio.org/mailman/listinfo/emboss http://emboss.open-bio.org/mailman/listinfo/emboss-dev http://emboss.open-bio.org/mailman/listinfo/emboss-announce http://emboss.open-bio.org/mailman/listinfo/emboss-bug The new FTP server is at: ftp://emboss.open-bio.org/pub/EMBOSS Alan From cjt01 at uark.edu Mon Jul 18 20:41:53 2005 From: cjt01 at uark.edu (C Thomas) Date: Mon, 18 Jul 2005 19:41:53 -0500 Subject: [emboss-dev] obselete bug in ajnam.c? Message-ID: <0A213FC7-B7DF-498F-897C-06C7821FDFEA@uark.edu> I was hunting through the emboss-2.10 source, when I found the following code in ajnam.c, inside the namListParse() function, which parses the emboss.default file and builds database definitions, environment definitions, etc.... at about line 1195: if(ajStrChar(curword, -1) == ':') { /* if last character is : then its a keyword */ ajStrToLower(&curword); /* make it lower case */ namNoColon(&curword); db_input = namDbAttr(curword); if(db_input < 0) ajWarn("%S: bad attribute '%S' for database '%S'\n", namRootStr, curword, name); } else if(db_input >= 0) { /* So if keyword type has been set */ if(ajStrChar(curword, 0) == '\'') It seems to me that the else if statement will never be executed, since the only chance db_input will ever get to be changed from its initialized value of -1 is inside the body of the previous if statement. By the way, the way the original source code file was tab formatted visually hid the bug, because there the statements "if(db_input < 0)" and "else if(db_input >= 0)" were on the same tab level. That's more like a formatting bug ;) Maybe this has already been rewritten in the new CVS version, I don't know because I only use the 2.10 version. Or maybe I'm mistaken and it isn't even a bug. Hope this is useful. C. Thomas From pmr at ebi.ac.uk Fri Jul 22 11:00:01 2005 From: pmr at ebi.ac.uk (Peter Rice) Date: Fri, 22 Jul 2005 16:00:01 +0100 Subject: [emboss-dev] EMBOSS in August Message-ID: <42E109F1.9070604@ebi.ac.uk> We know it is close to the end of July, and we have not said what is happening to the EMBOSS team. We do have a solution, but it is not yet officially confirmed. The Rosalind Franklin Centre for Genomic Research will close at the end of next week. The EMBOSS project will move to the European Bioinformatics Institute from August 1st. Development and support will continue as before. The EMBOSS homepage will remain at http://emboss.sourceforge.net/ The FTP server (to download EMBOSS releases and updates) has moved to ftp://emboss.open-bio.org/pub/EMBOSS/ The EMBOSS anonymous CVS server will remain at cvs.open-bio.org hosted by the Open Bio Foundation, who will also continue to host the developers' CVS server. The EMBOSS mailing lists have been moved to the Open Bio Foundation, so the addresses are now: To contact the EMBOSS team: emboss-bug at emboss.open-bio.org Bug reports and support requests emboss-submit at emboss.open-bio.org Code submissions Lists users/developers can subscribe to: emboss at emboss.open-bio.org Users mailing list emboss-dev at emboss.open-bio.org Developers mailing list emboss-announce at emboss.open-bio.org New release announcements list There are obvious gaps in these details ... more news as soon as we have confirmation. regards, Peter Rice, Alan Bleasby and the EMBOSS team. From cjt01 at uark.edu Sun Jul 24 21:44:42 2005 From: cjt01 at uark.edu (C Thomas) Date: Sun, 24 Jul 2005 20:44:42 -0500 Subject: [emboss-dev] number of sequences in a database Message-ID: <95E08C7C-57D6-4451-BE00-8E0C288AFACB@uark.edu> After I index a database for use with emboss, is there an ajax API call to find the total number of sequences in that database? I imagine that there's not a general way to get the total number of hits from a seqall object, since it looks like the sequences are discovered with each call to ajSeqallNext(). Am I right about that? regards, c. thomas From ableasby at hgmp.mrc.ac.uk Mon Jul 25 02:22:20 2005 From: ableasby at hgmp.mrc.ac.uk (Alan Bleasby) Date: Mon, 25 Jul 2005 07:22:20 +0100 (BST) Subject: [emboss-dev] number of sequences in a database Message-ID: <200507250622.j6P6MKQX003469@bromine.hgmp.mrc.ac.uk> There is no API call, as yet, to find the total number of sequences in a database - although this can be easily implemented for the dbx* indexing programs. If you have indexed using the dbx* programs then you can find the number of sequences by 'cat'ing the '.pxid' index file. HTH Alan From pmr at ebi.ac.uk Mon Jul 25 05:35:08 2005 From: pmr at ebi.ac.uk (Peter Rice) Date: Mon, 25 Jul 2005 10:35:08 +0100 Subject: [emboss-dev] number of sequences in a database In-Reply-To: <95E08C7C-57D6-4451-BE00-8E0C288AFACB@uark.edu> References: <95E08C7C-57D6-4451-BE00-8E0C288AFACB@uark.edu> Message-ID: <42E4B24C.6090808@ebi.ac.uk> C Thomas wrote: > After I index a database for use with emboss, is there an ajax API > call to find the total number of sequences in that database? There are scripts in the CVS scripts/ directory: If you CD to the database directory, the dbitest.pl script can report on the contents of database files. We use them for debugging. For example: ~/emboss/scripts/dbitest.pl entrynam.idx | more File size: 1136 Record count: 44 Record size: 19 Database name: 'EMBL' Release: '2.10' Shows there are 44 records (entries) in the database for the tembl database. You can find the script on our anonymous CVS server at http://cvs.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/emboss/emboss/scripts/dbitest.pl?cvsroot=emboss (I hope my mailer wraps that correctly :-) > I imagine that there's not a general way to get the total number of > hits from a seqall object, since it looks like the sequences are > discovered with each call to ajSeqallNext(). > Am I right about that? No general call ... some of the database access methods can easily do this, others cannot. Most of them can ... so perhaps we can add a call. For methods that have problems .... they can refuse, or read every entry to count them. Hope that helps, Peter From ableasby at hgmp.mrc.ac.uk Wed Jul 13 14:37:40 2005 From: ableasby at hgmp.mrc.ac.uk (Alan Bleasby) Date: Wed, 13 Jul 2005 15:37:40 +0100 (BST) Subject: [emboss-dev] New email lists ready Message-ID: <200507131437.j6DEbe8r027649@bromine.hgmp.mrc.ac.uk> The new email addresses for the EMBOSS lists are now set up and ready (excluding any teething problems). They are: emboss at emboss.open-bio.org emboss-dev at emboss.open-bio.org emboss-bug at emboss.open-bio.org emboss-submit at emboss.open-bio.org You can access the archives, subscribe/unsubscribe and alter the way email is sent to you (e.g. digests) by visiting: http://emboss.open-bio.org/mailman/listinfo/emboss http://emboss.open-bio.org/mailman/listinfo/emboss-dev http://emboss.open-bio.org/mailman/listinfo/emboss-announce http://emboss.open-bio.org/mailman/listinfo/emboss-bug The new FTP server is at: ftp://emboss.open-bio.org/pub/EMBOSS Alan From cjt01 at uark.edu Tue Jul 19 00:41:53 2005 From: cjt01 at uark.edu (C Thomas) Date: Mon, 18 Jul 2005 19:41:53 -0500 Subject: [emboss-dev] obselete bug in ajnam.c? Message-ID: <0A213FC7-B7DF-498F-897C-06C7821FDFEA@uark.edu> I was hunting through the emboss-2.10 source, when I found the following code in ajnam.c, inside the namListParse() function, which parses the emboss.default file and builds database definitions, environment definitions, etc.... at about line 1195: if(ajStrChar(curword, -1) == ':') { /* if last character is : then its a keyword */ ajStrToLower(&curword); /* make it lower case */ namNoColon(&curword); db_input = namDbAttr(curword); if(db_input < 0) ajWarn("%S: bad attribute '%S' for database '%S'\n", namRootStr, curword, name); } else if(db_input >= 0) { /* So if keyword type has been set */ if(ajStrChar(curword, 0) == '\'') It seems to me that the else if statement will never be executed, since the only chance db_input will ever get to be changed from its initialized value of -1 is inside the body of the previous if statement. By the way, the way the original source code file was tab formatted visually hid the bug, because there the statements "if(db_input < 0)" and "else if(db_input >= 0)" were on the same tab level. That's more like a formatting bug ;) Maybe this has already been rewritten in the new CVS version, I don't know because I only use the 2.10 version. Or maybe I'm mistaken and it isn't even a bug. Hope this is useful. C. Thomas From pmr at ebi.ac.uk Fri Jul 22 15:00:01 2005 From: pmr at ebi.ac.uk (Peter Rice) Date: Fri, 22 Jul 2005 16:00:01 +0100 Subject: [emboss-dev] EMBOSS in August Message-ID: <42E109F1.9070604@ebi.ac.uk> We know it is close to the end of July, and we have not said what is happening to the EMBOSS team. We do have a solution, but it is not yet officially confirmed. The Rosalind Franklin Centre for Genomic Research will close at the end of next week. The EMBOSS project will move to the European Bioinformatics Institute from August 1st. Development and support will continue as before. The EMBOSS homepage will remain at http://emboss.sourceforge.net/ The FTP server (to download EMBOSS releases and updates) has moved to ftp://emboss.open-bio.org/pub/EMBOSS/ The EMBOSS anonymous CVS server will remain at cvs.open-bio.org hosted by the Open Bio Foundation, who will also continue to host the developers' CVS server. The EMBOSS mailing lists have been moved to the Open Bio Foundation, so the addresses are now: To contact the EMBOSS team: emboss-bug at emboss.open-bio.org Bug reports and support requests emboss-submit at emboss.open-bio.org Code submissions Lists users/developers can subscribe to: emboss at emboss.open-bio.org Users mailing list emboss-dev at emboss.open-bio.org Developers mailing list emboss-announce at emboss.open-bio.org New release announcements list There are obvious gaps in these details ... more news as soon as we have confirmation. regards, Peter Rice, Alan Bleasby and the EMBOSS team. From cjt01 at uark.edu Mon Jul 25 01:44:42 2005 From: cjt01 at uark.edu (C Thomas) Date: Sun, 24 Jul 2005 20:44:42 -0500 Subject: [emboss-dev] number of sequences in a database Message-ID: <95E08C7C-57D6-4451-BE00-8E0C288AFACB@uark.edu> After I index a database for use with emboss, is there an ajax API call to find the total number of sequences in that database? I imagine that there's not a general way to get the total number of hits from a seqall object, since it looks like the sequences are discovered with each call to ajSeqallNext(). Am I right about that? regards, c. thomas From ableasby at hgmp.mrc.ac.uk Mon Jul 25 06:22:20 2005 From: ableasby at hgmp.mrc.ac.uk (Alan Bleasby) Date: Mon, 25 Jul 2005 07:22:20 +0100 (BST) Subject: [emboss-dev] number of sequences in a database Message-ID: <200507250622.j6P6MKQX003469@bromine.hgmp.mrc.ac.uk> There is no API call, as yet, to find the total number of sequences in a database - although this can be easily implemented for the dbx* indexing programs. If you have indexed using the dbx* programs then you can find the number of sequences by 'cat'ing the '.pxid' index file. HTH Alan From pmr at ebi.ac.uk Mon Jul 25 09:35:08 2005 From: pmr at ebi.ac.uk (Peter Rice) Date: Mon, 25 Jul 2005 10:35:08 +0100 Subject: [emboss-dev] number of sequences in a database In-Reply-To: <95E08C7C-57D6-4451-BE00-8E0C288AFACB@uark.edu> References: <95E08C7C-57D6-4451-BE00-8E0C288AFACB@uark.edu> Message-ID: <42E4B24C.6090808@ebi.ac.uk> C Thomas wrote: > After I index a database for use with emboss, is there an ajax API > call to find the total number of sequences in that database? There are scripts in the CVS scripts/ directory: If you CD to the database directory, the dbitest.pl script can report on the contents of database files. We use them for debugging. For example: ~/emboss/scripts/dbitest.pl entrynam.idx | more File size: 1136 Record count: 44 Record size: 19 Database name: 'EMBL' Release: '2.10' Shows there are 44 records (entries) in the database for the tembl database. You can find the script on our anonymous CVS server at http://cvs.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/emboss/emboss/scripts/dbitest.pl?cvsroot=emboss (I hope my mailer wraps that correctly :-) > I imagine that there's not a general way to get the total number of > hits from a seqall object, since it looks like the sequences are > discovered with each call to ajSeqallNext(). > Am I right about that? No general call ... some of the database access methods can easily do this, others cannot. Most of them can ... so perhaps we can add a call. For methods that have problems .... they can refuse, or read every entry to count them. Hope that helps, Peter