From skonietz at CeBiTec.Uni-Bielefeld.DE Fri Mar 24 07:33:17 2006 From: skonietz at CeBiTec.Uni-Bielefeld.DE (Sebastian Konietzny) Date: Fri, 24 Mar 2006 13:33:17 +0100 Subject: [emboss-dev] Bio-Emboss: executing "diffseq" as a perl function Message-ID: <4423E70D.1060501@CeBiTec.Uni-Bielefeld.DE> Hello! I would like to know how I can use Bio::Emboss in such a way, that I will not longer have to execute the "diffseq"-command as a system-call. I heard that it ought to be possible to use emboss-tools from inside a perl-script without system-calls but by using Emboss perl functions instead. Can anyone help me and explain, what would be the right subroutine and how I have to manage it's call? I also still ave problems to use the Bio::Emboss package in general. Thank you very much. From P.Ernst at dkfz-heidelberg.de Fri Mar 24 10:02:28 2006 From: P.Ernst at dkfz-heidelberg.de (Peter Ernst) Date: Fri, 24 Mar 2006 16:02:28 +0100 (CET) Subject: [emboss-dev] Bio-Emboss: executing "diffseq" as a perl function In-Reply-To: <4423E70D.1060501@CeBiTec.Uni-Bielefeld.DE> References: <4423E70D.1060501@CeBiTec.Uni-Bielefeld.DE> Message-ID: On Fri, 24 Mar 2006, Sebastian Konietzny wrote: > I would like to know how I can use Bio::Emboss in such a way, that I > will not longer have to execute the "diffseq"-command as a system-call. > > I heard that it ought to be possible to use emboss-tools from inside a > perl-script without system-calls but by using Emboss perl functions > instead. Can anyone help me and explain, what would be the right > subroutine and how I have to manage it's call? Bio::Emboss provides a Perl-API to the Emboss libraries, but not to the Emboss tools. A few Emboss tools, like "seqret", rely in their functionality almost completely in one or two library calls, and can therefore be easily copied to Perl. The "diffseq" tool, however, does a lot more than just calling a few library functions. If you would translate the diffseq.c source code line-by-line into Perl (what I do not recommend; too much work), the Bio::Emboss module would provide the interface to the Emboss functions like embWordBuildMatchTable(). If you *really* need a Perl-API for "diffseq", 1st) create a C library based on diffseq.c, providing the function you would like to use from Perl. 2nd) Use PerlXS, to interface from Perl to this library. (this is what Bio::Emboss does for the Emboss libraries) Kind regards, Peter -- Peter Ernst Department of Molecular Biophysics - B020 Deutsches Krebsforschungszentrum (German Cancer Research Center) DKFZ From dag at sonsorol.org Sat Mar 25 18:50:57 2006 From: dag at sonsorol.org (Chris Dagdigian) Date: Sat, 25 Mar 2006 18:50:57 -0500 Subject: [emboss-dev] Important news for developers on open-bio machines Message-ID: <1BB8AE37-91CA-45C7-AA81-A12826D5F422@sonsorol.org> Hi, apologies for the massive cross-post. I'll keep it short! This message is a last-ditch attempt to contact people with developer accounts on pub.open-bio.org who may have not received the individual mails we've been sending via the obf-developers at lists.open-bio.org mailing list. We suspect that there are a number of devs out there for whom we don't have up to date email addresses. All open-bio services have been migrated to new hardware and a new datacenter. Part of this migration process involved moving all developer accounts and all source-code repositories to a new server. The developer migration was completed a few minutes ago. An unavoidable side effect of the move is that all developers are now locked out of their accounts until they contact us for a password reset. If you are a developer and this news comes as a surprise to you, it means we don't have your contact info. Your best way to get up to speed on the history and technical details behind the migration is to point your browser here: http://lists.open-bio.org/mailman/private/obf-developers/2006-March/ thread.html ... and read the various messages we've posted this month. Included in the first message is the information on how to request an account reset. Regards, Chris Dagdigian open-bio.org From skonietz at CeBiTec.Uni-Bielefeld.DE Fri Mar 24 12:33:17 2006 From: skonietz at CeBiTec.Uni-Bielefeld.DE (Sebastian Konietzny) Date: Fri, 24 Mar 2006 13:33:17 +0100 Subject: [emboss-dev] Bio-Emboss: executing "diffseq" as a perl function Message-ID: <4423E70D.1060501@CeBiTec.Uni-Bielefeld.DE> Hello! I would like to know how I can use Bio::Emboss in such a way, that I will not longer have to execute the "diffseq"-command as a system-call. I heard that it ought to be possible to use emboss-tools from inside a perl-script without system-calls but by using Emboss perl functions instead. Can anyone help me and explain, what would be the right subroutine and how I have to manage it's call? I also still ave problems to use the Bio::Emboss package in general. Thank you very much. From P.Ernst at dkfz-heidelberg.de Fri Mar 24 15:02:28 2006 From: P.Ernst at dkfz-heidelberg.de (Peter Ernst) Date: Fri, 24 Mar 2006 16:02:28 +0100 (CET) Subject: [emboss-dev] Bio-Emboss: executing "diffseq" as a perl function In-Reply-To: <4423E70D.1060501@CeBiTec.Uni-Bielefeld.DE> References: <4423E70D.1060501@CeBiTec.Uni-Bielefeld.DE> Message-ID: On Fri, 24 Mar 2006, Sebastian Konietzny wrote: > I would like to know how I can use Bio::Emboss in such a way, that I > will not longer have to execute the "diffseq"-command as a system-call. > > I heard that it ought to be possible to use emboss-tools from inside a > perl-script without system-calls but by using Emboss perl functions > instead. Can anyone help me and explain, what would be the right > subroutine and how I have to manage it's call? Bio::Emboss provides a Perl-API to the Emboss libraries, but not to the Emboss tools. A few Emboss tools, like "seqret", rely in their functionality almost completely in one or two library calls, and can therefore be easily copied to Perl. The "diffseq" tool, however, does a lot more than just calling a few library functions. If you would translate the diffseq.c source code line-by-line into Perl (what I do not recommend; too much work), the Bio::Emboss module would provide the interface to the Emboss functions like embWordBuildMatchTable(). If you *really* need a Perl-API for "diffseq", 1st) create a C library based on diffseq.c, providing the function you would like to use from Perl. 2nd) Use PerlXS, to interface from Perl to this library. (this is what Bio::Emboss does for the Emboss libraries) Kind regards, Peter -- Peter Ernst Department of Molecular Biophysics - B020 Deutsches Krebsforschungszentrum (German Cancer Research Center) DKFZ From dag at sonsorol.org Sat Mar 25 23:50:57 2006 From: dag at sonsorol.org (Chris Dagdigian) Date: Sat, 25 Mar 2006 18:50:57 -0500 Subject: [emboss-dev] Important news for developers on open-bio machines Message-ID: <1BB8AE37-91CA-45C7-AA81-A12826D5F422@sonsorol.org> Hi, apologies for the massive cross-post. I'll keep it short! This message is a last-ditch attempt to contact people with developer accounts on pub.open-bio.org who may have not received the individual mails we've been sending via the obf-developers at lists.open-bio.org mailing list. We suspect that there are a number of devs out there for whom we don't have up to date email addresses. All open-bio services have been migrated to new hardware and a new datacenter. Part of this migration process involved moving all developer accounts and all source-code repositories to a new server. The developer migration was completed a few minutes ago. An unavoidable side effect of the move is that all developers are now locked out of their accounts until they contact us for a password reset. If you are a developer and this news comes as a surprise to you, it means we don't have your contact info. Your best way to get up to speed on the history and technical details behind the migration is to point your browser here: http://lists.open-bio.org/mailman/private/obf-developers/2006-March/ thread.html ... and read the various messages we've posted this month. Included in the first message is the information on how to request an account reset. Regards, Chris Dagdigian open-bio.org