From jbdundas at gmail.com Tue Oct 14 10:10:32 2008 From: jbdundas at gmail.com (jitesh dundas) Date: Tue, 14 Oct 2008 19:40:32 +0530 Subject: [emboss-dev] Fwd: Request For Work In-Reply-To: <48A2EE06.3050708@ebi.ac.uk> References: <326ea8620807300515n521c4f1ekf9042983fbc136f5@mail.gmail.com> <326ea8620807300531o43c7d25emad126ac26f0c376a@mail.gmail.com> <9F3EABD6E3419B4C81F34EAABB4D40181BF50DD2@irsmsx501.ger.corp.intel.com> <326ea8620808091218t12a6f1e8xd5354e9b585dc8ff@mail.gmail.com> <489EC516.7040105@ebi.ac.uk> <326ea8620808130712m6acd991bj5d0bea5727b7c21a@mail.gmail.com> <48A2EE06.3050708@ebi.ac.uk> Message-ID: <326ea8620810140710m355d3c6cydaad03bafe2dbf12@mail.gmail.com> Dear Sir, I apologize for dissappearing from the activity after assuring to work on this issue of trying to parallelize the EMBOSS project. I was not feeling well and have not been able to work for 1-2 months. I am fine now and will start working right now. By the way, I want to congratulate you for getting the funding from BBSRC( I saw on one of the science blogs).I hope we can continue to contribute on this wonderful project. I wanted to know the algorithm used in making the EMBOSS software. Maybe we can fine tune the algorithm to getting better and longer patterns... Any advise is most welcome. Regards, Jitesh Dundas On Wed, Aug 13, 2008 at 7:51 PM, Peter Rice wrote: > Dear jitesh, > > Thank you for your reply. Please excuse me for the delay in replying as I >> was out of town. >> I am looking at working on this issue in 2 ways:- >> 1) I wish to parallelize the phases of different softwares( if they are in >> develpment stage). >> 2) Next, if there is a connection or dependency between two or more >> projects( or applications), then we can try to give the output that is >> needed based on the current status of the output-supplying application. >> > > Aha ... so you are looking at running several EMBOSS applications in > parallel? That is a very interesting issue for us. > > I will need to know if there is any relationship identified between any of >> the applications defined in the EMBOSS project. If there are any >> relations >> already present between the applications, it will become easier to get a >> handle to move the execution from one point to another. >> > > The inputs and outputs of all EMBOSS applications are marked up in the .acd > files with a "knowntype" that identifies common outputs that could, for > example, be combined and visuallised together - and also which ooutput could > be used as inputs by other applications. For sequences, features, alignments > and reports this includes whether the type is nucleotide or protein. > > Also, Running applications in parallel will require a change in the way we >> make our applications. We need to define a master relationship between all >> the apllications, so as to relate all the applications with each other. >> > > We are also looking at adding definitions for the algorithm used by an > applications, and a standard way to represent the transformations of inputs > into outputs. > > Any feedback on these issues would be very welcome. > > We are also interested in looking at executing EMBOSS code in parallel is > anyone is looking at that. > > > regards, > > Peter Rice > From Sebastien.Moretti at unil.ch Wed Oct 22 10:27:56 2008 From: Sebastien.Moretti at unil.ch (Sebastien Moretti) Date: Wed, 22 Oct 2008 16:27:56 +0200 Subject: [emboss-dev] density Message-ID: <48FF386C.6030507@unil.ch> Hi, According to the ACD file, the density application seems to use the 'graph' qualifier. When used, I get this error message: Unknown qualifier -graph=colourps graph seems to have been replaced by ggraph and dgraph. And colourps seems to be cps now. How to fix it in the source ? Thanks -- S?bastien Moretti SIB EMBnet, Quartier Sorge - Genopode CH-1015 Lausanne, Switzerland Tel.: +41 (21) 692 4056/4221 http://ch.embnet.org/ http://myhits.vital-it.ch/ From njoly at pasteur.fr Thu Oct 23 15:20:00 2008 From: njoly at pasteur.fr (Nicolas Joly) Date: Thu, 23 Oct 2008 21:20:00 +0200 Subject: [emboss-dev] USA syntax and `%' character in sequence file names Message-ID: <20081023192000.GA222588@medusa.sis.pasteur.fr> Hi, We recently had a problem with a user that tried to use filenames that contains `%' characters on our UNIX servers ... It does not seems to work as expected, EMBOSS applications truncate the file name to be used. njoly at lanfeust [tmp/geecee]> rm -f foo%bar.data && touch foo%bar.data njoly at lanfeust [tmp/geecee]> seqret -sequence=foo%bar.data -auto -stdout Error: failed to open filename 'foo' Error: Unable to read sequence 'foo%bar.data' Died: seqret terminated: Bad value for '-sequence' with -auto defined Removing the `%' character make this dummy test work as expected. njoly at lanfeust [tmp/geecee]> rm -f foobar.data && touch foobar.data njoly at lanfeust [tmp/geecee]> seqret -sequence=foobar.data -auto -stdout Error: Unable to read sequence 'foobar.data' Died: seqret terminated: Bad value for '-sequence' with -auto defined I checked the USA format documentation but did not find any clue. Do the `%' character has a special meaning in the USA syntax ? Thanks. -- Nicolas Joly Biological Software and Databanks. Institut Pasteur, Paris. From ajb at ebi.ac.uk Thu Oct 23 17:47:54 2008 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Thu, 23 Oct 2008 22:47:54 +0100 (BST) Subject: [emboss-dev] USA syntax and `%' character in sequence file names In-Reply-To: <20081023192000.GA222588@medusa.sis.pasteur.fr> References: <20081023192000.GA222588@medusa.sis.pasteur.fr> Message-ID: <39434.86.9.126.186.1224798474.squirrel@webmail.ebi.ac.uk> Hi Nicolas, What it does, given a USA like: foo%10 is to seek 10 bytes into file foo and try to start reading a sequence from there. It does not, however, currently check that what appears after the '%' is a valid number. I believe invalid numbers are equivalent to an offset of 0. I suspect it might have been intended as a useful debugging tool for the programmer rather than as something for the biologist. If we leave it as an option we ought to mention it the documentation in some form though. ATB Alan > > Hi, > > We recently had a problem with a user that tried to use filenames that > contains `%' characters on our UNIX servers ... It does not seems to > work as expected, EMBOSS applications truncate the file name to be > used. > > njoly at lanfeust [tmp/geecee]> rm -f foo%bar.data && touch foo%bar.data > njoly at lanfeust [tmp/geecee]> seqret -sequence=foo%bar.data -auto -stdout > Error: failed to open filename 'foo' > Error: Unable to read sequence 'foo%bar.data' > Died: seqret terminated: Bad value for '-sequence' with -auto defined > > Removing the `%' character make this dummy test work as expected. > > njoly at lanfeust [tmp/geecee]> rm -f foobar.data && touch foobar.data > njoly at lanfeust [tmp/geecee]> seqret -sequence=foobar.data -auto -stdout > Error: Unable to read sequence 'foobar.data' > Died: seqret terminated: Bad value for '-sequence' with -auto defined > > I checked the USA format documentation but did not find any clue. Do > the `%' character has a special meaning in the USA syntax ? > > Thanks. > > -- > Nicolas Joly > > Biological Software and Databanks. > Institut Pasteur, Paris. > _______________________________________________ > emboss-dev mailing list > emboss-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss-dev > From njoly at pasteur.fr Fri Oct 24 03:43:22 2008 From: njoly at pasteur.fr (Nicolas Joly) Date: Fri, 24 Oct 2008 09:43:22 +0200 Subject: [emboss-dev] USA syntax and `%' character in sequence file names In-Reply-To: <39434.86.9.126.186.1224798474.squirrel@webmail.ebi.ac.uk> References: <20081023192000.GA222588@medusa.sis.pasteur.fr> <39434.86.9.126.186.1224798474.squirrel@webmail.ebi.ac.uk> Message-ID: <20081024074322.GB216223@medusa.sis.pasteur.fr> On Thu, Oct 23, 2008 at 10:47:54PM +0100, ajb at ebi.ac.uk wrote: > Hi Nicolas, > > What it does, given a USA like: > > foo%10 > > is to seek 10 bytes into file foo and try to start > reading a sequence from there. It does not, however, currently check that > what appears after the '%' is a valid number. I believe invalid numbers > are equivalent to an offset of 0. > > I suspect it might have been intended as a useful debugging tool for > the programmer rather than as something for the biologist. > If we leave it as an option we ought to mention it the documentation > in some form though. Thanks, Alan. Personally, i would get rid of it. But if you plan to keep it, please check for valid numbers before using it. -- Nicolas Joly Biological Software and Databanks. Institut Pasteur, Paris.