From eelhaik at gmail.com Sun Oct 2 22:12:26 2005 From: eelhaik at gmail.com (Eran Elhaik) Date: Sun, 2 Oct 2005 21:12:26 -0500 Subject: [EMBOSS] back translate software developmet Message-ID: Dear Sir I read your post in the group discussion and i was wondering if you can help me. I am looking for a program that can back translate a protein to it's di-codons. You probably realize that the program will have to build a di-codon usage for that first. I have failed to find a program that does that or n-codons to that matter of fact. I was wondering if you know any program that does that. thank you Eran ____________________________________ Eran Elhaik: Lab Phone: (713) 743-2312 Doctoral Student University of Houston http://nsmn1.uh.edu/~dgraur/eran/main.htm ____________________________________ From ulrike.kaule at gmx.de Mon Oct 3 16:57:18 2005 From: ulrike.kaule at gmx.de (Ulrike Kaule) Date: Mon, 03 Oct 2005 22:57:18 +0200 Subject: [EMBOSS] rebaseextract: invalid withrefm file Message-ID: <43419B2E.50405@gmx.de> Hello, I want to install the rebase-database locally according to Emboss Admin Guide. So I downloaded the withrefm.510.Z- and proto510.Z-files from ftp://ftp.ebi.ac.uk/pub/databases/rebase/ But when starting rebaseextract I got the following error "error in rebaseextract.c at line 163 - invalid withrefm file" Hope that somebody could help me - thank you in advance Ulrike From ajb at ebi.ac.uk Mon Oct 3 18:28:20 2005 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Mon, 3 Oct 2005 23:28:20 +0100 (BST) Subject: [EMBOSS] rebaseextract: invalid withrefm file In-Reply-To: <43419B2E.50405@gmx.de> References: <43419B2E.50405@gmx.de> Message-ID: <52387.81.96.70.96.1128378500.squirrel@webmail.ebi.ac.uk> Dear Ulrike, Those files are OK but you have to uncompress them first. Type: gunzip withrefm.510.Z gunzip proto510.Z That will give you the withrefm.510 and proto.510 files. Use those with rebaseextract. HTH Alan Bleasby EBI From ronnieoc at gmail.com Tue Oct 4 07:56:06 2005 From: ronnieoc at gmail.com (Ronnie O) Date: Tue, 4 Oct 2005 07:56:06 -0400 Subject: [EMBOSS] Seqret and Stdout Message-ID: <6ceab7de0510040456r14eec7e2ta3a0bc6919c5c926@mail.gmail.com> Hello all, I posted a bit ago about a problem I thought I was having piping data to stdin using seqret. I have more thoroughly investigated my problem and I have actually narrowed it down to getting my application to capture stdout from seqret. Quite the opposite than my original idea, but I have learned and debugged a lot since then! From posting previously, i took advice to create and analyze the debug file. From looking at the dbg file, I can see that my sequence data is making it into seqret and the dbg file appears identical to one created if I run the following command from a terminal: cat testdna | ./seqret raw::stdin raw::stdout -filter -debug The sequence in file testdna is printed to the screen (stdout, i assume). I have the same sequence data being piped in via a Cocoa application on mac os x. Comparison of the dbg files shows that they are identical. From this deduction, I assume in both cases data is being sent to stdout. Considering all this, I was thinking the problem is the capturing of stdout by my cocoa app. My problem with this idea is that I have the same exact piping mechanism successfully capturing stdout from a perl script that just echoes the data back. So my question to the forum, is there a possibility that the stdout from seqret is being piped to dev/console or somewhere I could be missing it? I also considered it was maybe being piped to stderror, but I have a pipe set up to catch that too (which has successfully caught errors). I included the -filter argument so the "read and writes sequences" output doesnt get returned to my cocoa app, would this alter data output at all? Or can anyone tell me how I could access the STDOUT environmental variable to make sure my pipe call is resulting in data sent to stdout? I have debugged this with both apps, and I have a tight area where things could be going wrong. Any ideas? Thanks again to all! ........... Ronnie From msarachu at biol.unlp.edu.ar Tue Oct 4 13:14:44 2005 From: msarachu at biol.unlp.edu.ar (Martin Sarachu) Date: Tue, 04 Oct 2005 14:14:44 -0300 Subject: [EMBOSS] how to install help files with MYEMBOSS? Message-ID: <4342B884.5080204@biol.unlp.edu.ar> Dear all, is there any way to install help files (both text and html) for your custom applications using MYEMBOSS? I intend to modify wrappers4EMBOSS package to install using MYEMBOSS but I can't find a way to install the help files for them, just the source and acd files. There is no doc/programs... directory, is there another way of doing this? Thanks. Cheers, Martin -- Martin Sarachu msarachu at biol.unlp.edu.ar AR.EMBnet http://www.ar.embnet.org From pmr at ebi.ac.uk Tue Oct 4 13:44:36 2005 From: pmr at ebi.ac.uk (pmr at ebi.ac.uk) Date: Tue, 4 Oct 2005 18:44:36 +0100 (BST) Subject: [EMBOSS] how to install help files with MYEMBOSS? In-Reply-To: <4342B884.5080204@biol.unlp.edu.ar> References: <4342B884.5080204@biol.unlp.edu.ar> Message-ID: <4439.86.133.38.47.1128447876.squirrel@webmail.ebi.ac.uk> Dear Martin, > is there any way to install help files (both text and html) for your > custom applications using MYEMBOSS? > I intend to modify wrappers4EMBOSS package to install using MYEMBOSS but > I can't find a way to install the help files for them, just the source > and acd files. There is no doc/programs... directory, is there another > way of doing this? We will add these. There are plans to create separate directories for each of the EMBASSY packages (myemboss, phylip, domainatrix, hmmer, ...) under doc/programs instead of installing everything in one directory. We waited for EMBOSS 3.0.0 before trying to reorganize. One issue for the MYEMBOSS documentation ... we create the documentation from the sourceforge pages for each applicatiion. We will need a utility to complete the pages for MYEMBOSS programs which are written locally and will not have sourceforge pages as sources. These sourceforge pages have 9 include files (the one line documentation, help and commandline table, example usage with input and output, related programs plus history and comments. We can generate all these include files automatically. If you have example MYEMBOSS programs you can send it would help us to make producing the documentation easier. regards, Peter Rice From msarachu at biol.unlp.edu.ar Tue Oct 4 14:34:46 2005 From: msarachu at biol.unlp.edu.ar (Martin Sarachu) Date: Tue, 04 Oct 2005 15:34:46 -0300 Subject: [EMBOSS] how to install help files with MYEMBOSS? In-Reply-To: <4439.86.133.38.47.1128447876.squirrel@webmail.ebi.ac.uk> References: <4342B884.5080204@biol.unlp.edu.ar> <4439.86.133.38.47.1128447876.squirrel@webmail.ebi.ac.uk> Message-ID: <4342CB46.9020900@biol.unlp.edu.ar> Dear Peter, I can send the documentation for all wrappers4EMBOSS (BLAST, fastA, MUSCLE, etc) programs. Do you want me to send these to you? Regards, Martin pmr at ebi.ac.uk wrote: > Dear Martin, > > >>is there any way to install help files (both text and html) for your >>custom applications using MYEMBOSS? >>I intend to modify wrappers4EMBOSS package to install using MYEMBOSS but >>I can't find a way to install the help files for them, just the source >>and acd files. There is no doc/programs... directory, is there another >>way of doing this? > > > We will add these. There are plans to create separate directories for each > of the EMBASSY packages (myemboss, phylip, domainatrix, hmmer, ...) under > doc/programs instead of installing everything in one directory. We waited > for EMBOSS 3.0.0 before trying to reorganize. > > One issue for the MYEMBOSS documentation ... we create the documentation > from the sourceforge pages for each applicatiion. We will need a utility > to complete the pages for MYEMBOSS programs which are written locally and > will not have sourceforge pages as sources. These sourceforge pages have 9 > include files (the one line documentation, help and commandline table, > example usage with input and output, related programs plus history and > comments. We can generate all these include files automatically. > > If you have example MYEMBOSS programs you can send it would help us to > make producing the documentation easier. > > regards, > > Peter Rice > -- Martin Sarachu msarachu at biol.unlp.edu.ar AR.EMBnet http://www.ar.embnet.org From smiddha at cgb.indiana.edu Thu Oct 6 12:21:20 2005 From: smiddha at cgb.indiana.edu (Sumit Middha) Date: Thu, 06 Oct 2005 11:21:20 -0500 Subject: [EMBOSS] Embassy tools In-Reply-To: <56436.81.96.71.66.1126247494.squirrel@webmail.ebi.ac.uk> References: <39102.129.111.174.49.1124381885.squirrel@biochem.uthscsa.edu> <4320790C.6090508@indiana.edu> <56436.81.96.71.66.1126247494.squirrel@webmail.ebi.ac.uk> Message-ID: <43454F00.2050103@cgb.indiana.edu> Hello Alan, Thanks for your help on that. I tried downloading and installing mse-1.0. The make was going fine until this error. A similar thing happened with MYEMBOSS-3.0. I used the --prefix option for emboss. So I untarred these to someplace and used .configure with --prefix option. Am I doing something wrong? Thanks. mse.c:18:18: ajax.h: No such file or directory In file included from mse.c:29: ../h/mse.h:203: error: parse error before "AjPSeqout" mse.c:40: error: parse error before "seqset" mse.c: In function `LoadSeqWithseqset': mse.c:43: error: syntax error before "tempname" mse.c:45: error: `seqset' undeclared (first use in this function) mse.c:45: error: (Each undeclared identifier is reported only once mse.c:45: error: for each function it appears in.) mse.c:51: warning: passing arg 2 of `strcpy' makes pointer from integer without a cast mse.c:54: warning: assignment makes pointer from integer without a cast mse.c:77: error: `tempname' undeclared (first use in this function) mse.c:79: warning: passing arg 2 of `strcpy' makes pointer from integer without a cast mse.c: At top level: mse.c:100: error: parse error before "AjPSeqout" mse.c: In function `DoSave': mse.c:104: error: `AjPSeq' undeclared (first use in this function) mse.c:104: error: parse error before "seqnew" mse.c:105: error: `AjPStr' undeclared (first use in this function) mse.c:106: error: `AjPSeqout' undeclared (first use in this function) ......... *** Error code 1 make: Fatal error: Command failed for target `mse.o' Current working directory /bioportal/build/MSE-1.0.0/source *** Error code 1 make: Fatal error: Command failed for target `all-recursive' for MYEMBOSS: myseq.c:22:20: emboss.h: No such file or directory myseq.c: In function `main': myseq.c:33: error: `AjPSeq' undeclared (first use in this function) myseq.c:33: error: (Each undeclared identifier is reported only once myseq.c:33: error: for each function it appears in.) ......... ajb at ebi.ac.uk wrote: >There are also instructions at: > http://emboss.sourceforge.net/docs/faq.html > >Look for "Q) Installing associated software PHYLIP". You need the >instructions >in part 'b)' of that question as you are not using the CVS version of EMBOSS. > >To summarise what's there in case it was that documentation which >confused you, if you installed EMBOSS-3.0.0 using: > > ./configure --prefix=/usr/local/emboss [and any other options you chose] > make > make install > >Then you install PHYLIP using: > > ./configure --prefix=/usr/local/emboss [and any other options you chose] > make > make install > > > >There is only one exception and that is if you installed EMBOSS-3.0.0 using: > > ./configure > make > make install > >(i.e. you didn't supply a --prefix). In this case you have to supply >an extra flag to the EMBASSY package configuration i.e. > > ./configure --enable-localforce > make > make install > >We recommend that you use the first approach (i.e supply a --prefix) >to have EMBOSS installed in a directory of its own. >The instructions at the URL above were updated last night and replace >those in the EMBOSS-3.0.0/FAQ file. > >HTH > >Alan > > > > -- Sumit Middha, MS in Bioinformatics Assistant Staff Scientist The Center for Genomics and Bioinformatics Indiana University, Jordan Hall Bloomington, IN 47405-3700 From enrique.deandres at pcm.uam.es Thu Oct 13 04:37:35 2005 From: enrique.deandres at pcm.uam.es (Enrique de Andres Saiz) Date: Thu, 13 Oct 2005 10:37:35 +0200 Subject: [EMBOSS] Segmentation fault when doing seqret Message-ID: <434E1CCF.5030206@pcm.uam.es> Hello, I'm trying to retrieve a sequence from embl using seqret command but I obtain a segmentation fault error: $> seqret embl:AC005155 Reads and writes (returns) sequences Segmentation fault This doesn't happen with every entry in the database. With another entries, everything goes well. I'm using emboss-3.0.0 and EMBL database is indexed using dbiflat. Does anybody konws what could happen? Thanks in advance, Enrique. From isabelle.wells at roche.com Thu Oct 13 04:46:48 2005 From: isabelle.wells at roche.com (Wells, Isabelle) Date: Thu, 13 Oct 2005 10:46:48 +0200 Subject: [EMBOSS] Segmentation fault when doing seqret Message-ID: Hi, Are any of the EMBL flat files larger than 2GB? This is a problem when indexing with dbiflat and was already discussed on this list. Isabelle -----Original Message----- From: emboss-bounces at emboss.open-bio.org [mailto:emboss-bounces at emboss.open-bio.org] On Behalf Of Enrique de Andres Saiz Sent: Thursday, October 13, 2005 10:38 To: emboss at emboss.open-bio.org Subject: [EMBOSS] Segmentation fault when doing seqret Hello, I'm trying to retrieve a sequence from embl using seqret command but I obtain a segmentation fault error: $> seqret embl:AC005155 Reads and writes (returns) sequences Segmentation fault This doesn't happen with every entry in the database. With another entries, everything goes well. I'm using emboss-3.0.0 and EMBL database is indexed using dbiflat. Does anybody konws what could happen? Thanks in advance, Enrique. _______________________________________________ EMBOSS mailing list EMBOSS at emboss.open-bio.org http://newportal.open-bio.org/mailman/listinfo/emboss From David.Bauer at SCHERING.DE Thu Oct 13 05:29:52 2005 From: David.Bauer at SCHERING.DE (David.Bauer at SCHERING.DE) Date: Thu, 13 Oct 2005 11:29:52 +0200 Subject: [EMBOSS] Segmentation fault when doing seqret In-Reply-To: Message-ID: Hi, you can try the new indexing system dbxflat. This indexer has no 2 Gb limit. David. emboss-bounces at emboss.open-bio.org schrieb am 13/10/2005 10:46:48: > Hi, > Are any of the EMBL flat files larger than 2GB? This is a problem when > indexing with dbiflat and was already discussed on this list. > Isabelle > > -----Original Message----- > From: emboss-bounces at emboss.open-bio.org > [mailto:emboss-bounces at emboss.open-bio.org] On Behalf Of Enrique de > Andres Saiz > Sent: Thursday, October 13, 2005 10:38 > To: emboss at emboss.open-bio.org > Subject: [EMBOSS] Segmentation fault when doing seqret > > > Hello, > > I'm trying to retrieve a sequence from embl using seqret command but I > obtain a segmentation fault error: > > $> seqret embl:AC005155 > Reads and writes (returns) sequences > Segmentation fault > > This doesn't happen with every entry in the database. With another > entries, everything goes well. > > I'm using emboss-3.0.0 and EMBL database is indexed using dbiflat. > > Does anybody konws what could happen? > > Thanks in advance, > > Enrique. > _______________________________________________ > EMBOSS mailing list > EMBOSS at emboss.open-bio.org > http://newportal.open-bio.org/mailman/listinfo/emboss > > _______________________________________________ > EMBOSS mailing list > EMBOSS at emboss.open-bio.org > http://newportal.open-bio.org/mailman/listinfo/emboss From easmith at beatrice.rutgers.edu Thu Oct 13 12:32:56 2005 From: easmith at beatrice.rutgers.edu (Allen Smith) Date: Thu, 13 Oct 2005 12:32:56 -0400 Subject: [EMBOSS] indexing of nr file with dbxfasta is missing some data Message-ID: I've used dbxfasta to index the NCBI nr database file of ~Sep 7 10:33 (as earlier reported - problems with filename of "nr" fixed by going to "nr.fasta", with a thank-you to Alan), with the idformat being ncbi. It doesn't seem to be picking up anything beyond the first ID - none of the same-sequence IDs added in with control-A's seperating them. -Allen seqret 'nr:ZP_00652394*' Reads and writes (returns) sequences Error: Unable to read sequence 'nr:ZP_00652394*' Died: seqret terminated: Bad value for '-sequence' and no prompt seqret 'nr:ZP_00682210*' Reads and writes (returns) sequences Output sequence [zp_00682210.fasta]: stdout >ZP_00682210.1 ZP_00682210.1 Zinc-containing alcohol dehydrogenase superfamily [Xylella fastidiosa Ann-1]gi|71730149|gb|EAO32237.1| Zinc-containing alcohol dehydrogenase superfamily [Xylella fastidiosa Ann-1]gi|71276114|ref|ZP_00652394.1| Zinc-containing alcohol dehydrogenase superfamily [Xylella fastidiosa Dixon]gi|71163032|gb|EAO12754.1| Zinc-containing alcohol dehydrogenase superfamily [Xylella fastidiosa Dixon] MFINAYGAHAGDKPLESMQIARRAPGVHDVQIDIHYCGVCHSDIHLVRSEWAGTLFPCVP GHEIVGRVSAIGTHVQGFKAGDLVAVGCMVDSCKDCQECDAGLENYCDGMIGTYNFPTQD APGHTLGGYSQKIVVHERFVLRIRHPEAQLAAVAPLLCAGITTYSPLRHWNAGPGKKVGI VGIGGLGHMGIKLAHAMGAYVVAFTTSESKRQDAKALGADEVVVSRDEERMAAHVKSFDL ILNTVAASHSLDPFLTLLKRDGTLTLVGAPATPHPSPEVFNLIFKRRSIAGSLIGGIAET QQMLDFCAKHGIVADIELIRADGINEAYERMMKGDVKYRFVIDNATLAA -- Allen Smith http://cesario.rutgers.edu/easmith/ February 1, 2003 Space Shuttle Columbia Ad Astra Per Aspera To The Stars Through Asperity safety." - Benjamin Franklin From enrique.deandres at pcm.uam.es Fri Oct 14 03:41:27 2005 From: enrique.deandres at pcm.uam.es (Enrique de Andres Saiz) Date: Fri, 14 Oct 2005 09:41:27 +0200 Subject: [EMBOSS] Segmentation fault when doing seqret In-Reply-To: References: Message-ID: <434F6127.5030106@pcm.uam.es> Thanks. Indeed, there are some files larger than 2GB in EMBL. As David said, I have tried with dbxflat and now it goes well. Regards, Enrique. Wells, Isabelle wrote: > Hi, > Are any of the EMBL flat files larger than 2GB? This is a problem when > indexing with dbiflat and was already discussed on this list. > Isabelle > > -----Original Message----- > From: emboss-bounces at emboss.open-bio.org > [mailto:emboss-bounces at emboss.open-bio.org] On Behalf Of Enrique de > Andres Saiz > Sent: Thursday, October 13, 2005 10:38 > To: emboss at emboss.open-bio.org > Subject: [EMBOSS] Segmentation fault when doing seqret > > > Hello, > > I'm trying to retrieve a sequence from embl using seqret command but I > obtain a segmentation fault error: > > $> seqret embl:AC005155 > Reads and writes (returns) sequences > Segmentation fault > > This doesn't happen with every entry in the database. With another > entries, everything goes well. > > I'm using emboss-3.0.0 and EMBL database is indexed using dbiflat. > > Does anybody konws what could happen? > > Thanks in advance, > > Enrique. > _______________________________________________ > EMBOSS mailing list > EMBOSS at emboss.open-bio.org > http://newportal.open-bio.org/mailman/listinfo/emboss > > > -- Enrique de Andr?s Saiz Unidad de Bioinform?tica Parque Cient?fico de Madrid Ctra. de Colmenar, Km. 15 Campus Universidad Aut?noma de Madrid, Cantoblanco - Pabell?n C 28049 Madrid Phone: +34 91 497 3448 Fax: +34 91 497 3471 E-mail: enrique.deandres at pcm.uam.es From ChitchaiH at afrims.org Sun Oct 16 21:35:50 2005 From: ChitchaiH at afrims.org (Chitchai, Hemachudha Mr USAMC-AFRIMS) Date: Mon, 17 Oct 2005 08:35:50 +0700 Subject: [EMBOSS] Unix vs. Windows Message-ID: <1A8F450C5B709D409671A973CECAC93701B33B00@afmlh405b2238.ad.afrims.org> Hello, I'm new to emboss. I'd like to know about the performance and benefits between running EMBOSS on Unix vs. Windows. Thank you. ch From yezhiqiang at gmail.com Mon Oct 17 03:21:56 2005 From: yezhiqiang at gmail.com (yezhiqiang at gmail.com) Date: Mon, 17 Oct 2005 15:21:56 +0800 Subject: [EMBOSS] A question about uniform sequence address (USA) Message-ID: <34198fe40510170021r4ae75faev@mail.gmail.com> Hi, dear all, As we all know, we can use USA grammar like this: Format::database:entryname[1:50]. This is referred to as first 1 to 50 residues (nt for dna) of entry "entryname" in database. But now I have a sequencial database(eg. a flatfile or fasta format sequence file), can we use the entry position (not the entry name ) to refer the entry? For example, how can I get the 5th sequence in the flatfile? Can USA handle this kind of request? Thanks. From ajb at ebi.ac.uk Mon Oct 17 04:20:16 2005 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Mon, 17 Oct 2005 09:20:16 +0100 (BST) Subject: [EMBOSS] A question about uniform sequence address (USA) In-Reply-To: <34198fe40510170021r4ae75faev@mail.gmail.com> References: <34198fe40510170021r4ae75faev@mail.gmail.com> Message-ID: <54351.172.31.100.157.1129537216.squirrel@webmail.ebi.ac.uk> This isn't built into the USA yet. There is, however, a program called 'nthseq' in the distribution which will do this. It is a little limited but may be enough for your needs. HTH Alan > Hi, dear all, > > As we all know, we can use USA grammar like this: > Format::database:entryname[1:50]. This is referred to as first 1 to 50 > residues (nt for dna) of entry "entryname" in database. > But now I have a sequencial database(eg. a flatfile or fasta > format sequence file), can we use the entry position (not the entry > name ) to refer the entry? For example, how can I get the 5th sequence > in the flatfile? Can USA handle this kind of request? > Thanks. > > _______________________________________________ > EMBOSS mailing list > EMBOSS at emboss.open-bio.org > http://newportal.open-bio.org/mailman/listinfo/emboss > From cquijano at iib.uam.es Mon Oct 17 06:29:30 2005 From: cquijano at iib.uam.es (Carlos Quijano) Date: Mon, 17 Oct 2005 12:29:30 +0200 Subject: [EMBOSS] Unix vs. Windows In-Reply-To: <1A8F450C5B709D409671A973CECAC93701B33B00@afmlh405b2238.ad.afri ms.org> References: <1A8F450C5B709D409671A973CECAC93701B33B00@afmlh405b2238.ad.afrim s.org> Message-ID: <1129544970.9118.15.camel@furthermore.iib.uam.es> El lun, 17-10-2005 a las 08:35 +0700, Chitchai, Hemachudha Mr USAMC-AFRIMS escribi?: > Hello, > > I'm new to emboss. > I'd like to know about the performance and benefits between running > EMBOSS on Unix vs. Windows. Performance is more related to hardware than operative system. For example, it is better to use an Athlon 64 dual core and 4Gb RAM with windows than a 32bit processor with 512Mb RAM and linux. But in bioinformatics, having the same hardware, using Linux is much more productive than windows, because of the lack of applications that are developed on windows with windows APIs and microsonft developing tools. Normally bioinformatic tools are developed on Linux, with linux APIs and developing tools and this translates in better performance under Linux operative system. The benefits of using Linux are well known, but in the bioinformatics field it is even more relevant. We use to process huge amounts of data and we need high performance computing. Moreover, most of the jobs that we execute in a workstation or a cluster are complicate but using the command-line can be mostly reduced to less than ten sentences, so we need a powerfull comand-line interface, and it is a very lack of windows' Windows is more friendly-use oriented, and then, it is interesting in the case of visualization and when a powerfull user interface is needed. But it is not a problem with Linux. I still agree that Linux is a wonderful field in wich developing new and promising user-interfaces should be a motivation. > > Thank you. > ch > > > _______________________________________________ > EMBOSS mailing list > EMBOSS at emboss.open-bio.org > http://newportal.open-bio.org/mailman/listinfo/emboss From yezhiqiang at gmail.com Mon Oct 17 04:53:18 2005 From: yezhiqiang at gmail.com (Zhiqiang Ye) Date: Mon, 17 Oct 2005 16:53:18 +0800 Subject: [EMBOSS] A question about uniform sequence address (USA) In-Reply-To: <54351.172.31.100.157.1129537216.squirrel@webmail.ebi.ac.uk> References: <34198fe40510170021r4ae75faev@mail.gmail.com> <54351.172.31.100.157.1129537216.squirrel@webmail.ebi.ac.uk> Message-ID: <34198fe40510170153m582fdbc8v@mail.gmail.com> Thank you, Alan. This helps. I noticed that tfm will cause very high load average when I type "tfm nthseq" This occurs when I "tfm" other programs. Systems tested: EMBOSS 3.0.0 on a Debian linux with kernel 2.6. EMBOSS 3.0.0 on a gentoo linux with kernel 2.6 EMBOSS 2.10.0 on a redhat linu with kernel 2.4 I am not sure what's the cause. 2005/10/17, ajb at ebi.ac.uk : > This isn't built into the USA yet. There is, however, a program called > 'nthseq' in the distribution which will do this. It is a little limited > but may be enough for your needs. > > HTH > > Alan > > > Hi, dear all, > > > > As we all know, we can use USA grammar like this: > > Format::database:entryname[1:50]. This is referred to as first 1 to 50 > > residues (nt for dna) of entry "entryname" in database. > > But now I have a sequencial database(eg. a flatfile or fasta > > format sequence file), can we use the entry position (not the entry > > name ) to refer the entry? For example, how can I get the 5th sequence > > in the flatfile? Can USA handle this kind of request? > > Thanks. > > > > _______________________________________________ > > EMBOSS mailing list > > EMBOSS at emboss.open-bio.org > > http://newportal.open-bio.org/mailman/listinfo/emboss > > > > > -- Zhiqiang Ye PHD candidate College of Lifesciences PKU, Beijing. From Peter.Robinson at t-online.de Fri Oct 21 07:37:59 2005 From: Peter.Robinson at t-online.de (Peter.Robinson at t-online.de) Date: Fri, 21 Oct 2005 13:37:59 +0200 Subject: [EMBOSS] Bootstrap with PHYLIP Message-ID: <1ESvDj-2Bfi4m0@fwd29.aul.t-online.de> An HTML attachment was scrubbed... URL: http://lists.open-bio.org/pipermail/emboss/attachments/20051021/572b6453/attachment.html From pmr at ebi.ac.uk Fri Oct 21 08:21:00 2005 From: pmr at ebi.ac.uk (Peter Rice) Date: Fri, 21 Oct 2005 13:21:00 +0100 Subject: [EMBOSS] Bootstrap with PHYLIP In-Reply-To: <1ESvDj-2Bfi4m0@fwd29.aul.t-online.de> References: <1ESvDj-2Bfi4m0@fwd29.aul.t-online.de> Message-ID: <4358DD2C.6070401@ebi.ac.uk> Dear Peter, Peter.Robinson at t-online.de wrote: > Dear EMBOSSers, > > I would like to use the EMBASSY programs of PHYLIP such as fdnadist to do > bootstrap analysis etc run by a sheel script. In the menudriven version of > PHYLIP, many of the programs have a menu item "M" where one can tell the program > how many datasets to use (e.g., dnadist). In the EMBASSY version, at least some > of the programs do not seem to have this; it is not documented on the website, > and an attempt to go > $ fdnadist -M 1000 -sequence test.fseqboot > does not work (where test.fseqboot contains 1000 boot strap datasets produced by > fseqboot). > Is this not yet implemented in the EMBASSY version or am I overseeing something? -M is a phylip option. All the options in PHYLIP are single letters, which do not work on the EMBOSS command line ... so you have to match the EMBOSS command line options with the PHYLIP menus. There are some PHYLIP options, M is one of them, which we do not need. M tells phylip to use multiple datasets from the input. The EMBOSS version fdnadist will read the datasets automatically, and will set M to the number of sequence sets (or number of weights). However ... I just tested this with the current version of fdnadist and found a bug on our Tru64 system. I suspect this was because I used the small test datasets that are provided in the PHYLIP documentation, but I am still investigating. Please try with your dataset and let me know if you have any problems. If anyone has some larger test datasets for the PHYLIP programs I would be very interested in trying fdnadist and the other programs to check we aer agreeing with the results from the native PHYLIP package. EMBOSS includes a beta release of PHYLIP 3.6 - we still have to update to the code changes in the most recent version. We plan to do this in the enxt few months. More bug reports will mean we do it faster - to make sure we have the latest code before bug hunting :-) Hope this helps, Peter Rice From biopyte at yahoo.de Sat Oct 22 08:15:31 2005 From: biopyte at yahoo.de (Hans Meier) Date: Sat, 22 Oct 2005 14:15:31 +0200 (CEST) Subject: [EMBOSS] "remap" as standalone app Message-ID: <20051022121531.21097.qmail@web26313.mail.ukl.yahoo.com> Dear friends, is it possible to use "remap" as a standalone application? That means, after compiling EMBOSS I'd like to delete everthing except the "remap"-binary. Of course, it's not that easy, because "remap" depends on libraries and the rebase-files. And "remap" has to know the path to these files. Maybe the libraries could be statically linked? Does anybody have a suggestion how to isolate a full functional "remap" from the EMBOSS package? Thanks, Harald ___________________________________________________________ Gesendet von Yahoo! Mail - Jetzt mit 1GB Speicher kostenlos - Hier anmelden: http://mail.yahoo.de From biopyte at yahoo.de Sat Oct 22 10:18:08 2005 From: biopyte at yahoo.de (Hans Meier) Date: Sat, 22 Oct 2005 16:18:08 +0200 (CEST) Subject: [EMBOSS] remap as standalone app Message-ID: <20051022141808.68961.qmail@web26303.mail.ukl.yahoo.com> Dear friends, is it possible to use "remap" as a standalone application? That means, after compiling EMBOSS I'd like to delete everthing except the "remap"-binary. Of course, it's not that easy, because "remap" depends on libraries and the rebase-files. And "remap" has to know the path to these files. Maybe the libraries could be statically linked? Does anybody have a suggestion how to isolate a full functional "remap" from the EMBOSS package? Thanks, Harald ___________________________________________________________ Gesendet von Yahoo! Mail - Jetzt mit 1GB Speicher kostenlos - Hier anmelden: http://mail.yahoo.de From pmr at ebi.ac.uk Sat Oct 22 10:33:47 2005 From: pmr at ebi.ac.uk (pmr at ebi.ac.uk) Date: Sat, 22 Oct 2005 15:33:47 +0100 (BST) Subject: [EMBOSS] "remap" as standalone app In-Reply-To: <20051022121531.21097.qmail@web26313.mail.ukl.yahoo.com> References: <20051022121531.21097.qmail@web26313.mail.ukl.yahoo.com> Message-ID: <1203.86.132.216.45.1129991627.squirrel@webmail.ebi.ac.uk> Dear Harald, > is it possible to use "remap" as a > standalone application? > That means, after compiling EMBOSS I'd like > to delete everthing except the "remap"-binary. > Of course, it's not that easy, because "remap" > depends on libraries and the rebase-files. > And "remap" has to know the path to these files. > Maybe the libraries could be statically linked? > Does anybody have a suggestion how to isolate > a full functional "remap" from the EMBOSS package? ./configure --help will give you a list of the extra options available. ./configure --disable-shared will build without shared libraries. This may be enough for remap. For EMBOSS graphical programs you will also need --without-X to disable linking to the X11 system libraries. We do not regularly test whether EMBOSS builds standalone, but I have done it in the past, and another user at EBI was trying exactly this procedure yesterday! Hope this helps Peter Rice From tmargus at ebc.ee Sun Oct 23 13:29:07 2005 From: tmargus at ebc.ee (=?iso-8859-1?Q?T=F5nu_Margus?=) Date: Sun, 23 Oct 2005 20:29:07 +0300 Subject: [EMBOSS] dbifasta and ncbi formats Message-ID: <200510231740.j9NHet38010303@newportal.open-bio.org> Hi, Sorry for trivial question. What are available ?formats? for ncbi fastA format ? ncbi (| formats) I don?t figure out, how to specify these (| formats) If I run dbifasta and choose ?idformat ncbi then after creating database index seqret returns sequences only when I specify NP_414542.1 and not by gi number. How can I use the gi number for retrival as well? Example header of FastA flatfile >gi|16127995|ref|NP_414542.1| thr operon leader peptide [Escherichia coli K12] AND Database definition is here DB ec [ type: P dir: /home/db/coli method: emblcd format: fasta file:ecoli_p.faa comment: "E.coli proteom from NCBI" ] Thanks Tonu From David.Bauer at SCHERING.DE Mon Oct 24 02:19:55 2005 From: David.Bauer at SCHERING.DE (David.Bauer at SCHERING.DE) Date: Mon, 24 Oct 2005 08:19:55 +0200 Subject: [EMBOSS] Antwort: dbifasta and ncbi formats In-Reply-To: <200510231740.j9NHet38010303@newportal.open-bio.org> Message-ID: Hi, the ncbi format is not fully supported by emboss. So you can only retrieve by the first acc (with version), not with gi and in case of nr (several entries separated by Ctrl-A) the other accs are also ignored. You can format the ncbi fasta file with formatdb -o T and then specify fastacmd as app in emboss. In the adminguide is a short description about external access methods: http://emboss.sourceforge.net/docs/adminguide/node4.html#SECTION00422150000000000000 Hope this helps, David. emboss-bounces at emboss.open-bio.org schrieb am 23/10/2005 19:29:07: > Hi, > > > > Sorry for trivial question. What are available ?formats? for ncbi fastA > format ? > > > ncbi > > (| formats) > > > > I don?t figure out, how to specify these (| formats) > > > > If I run dbifasta and choose ?idformat ncbi then after creating database > index seqret returns sequences only when I specify NP_414542.1 and not by gi > number. How can I use the gi number for retrival as well? > > > > Example header of FastA flatfile > > > > >gi|16127995|ref|NP_414542.1| thr operon leader peptide [Escherichia > coli K12] > > > > AND > > > > Database definition is here > > > > DB ec [ > > type: P > > dir: /home/db/coli > > method: emblcd > > format: fasta > > file:ecoli_p.faa > > comment: "E.coli proteom from NCBI" > > ] > > > > > > Thanks > > Tonu > > > _______________________________________________ > EMBOSS mailing list > EMBOSS at emboss.open-bio.org > http://newportal.open-bio.org/mailman/listinfo/emboss From easmith at beatrice.rutgers.edu Mon Oct 24 02:47:55 2005 From: easmith at beatrice.rutgers.edu (Allen Smith) Date: Mon, 24 Oct 2005 02:47:55 -0400 Subject: [EMBOSS] Antwort: dbifasta and ncbi formats In-Reply-To: References: <200510231740.j9NHet38010303@newportal.open-bio.org> Message-ID: In message (on 24 October 2005 08:19:55 +0200), David.Bauer at SCHERING.DE (David.Bauer at SCHERING.DE) wrote: > > >Hi, >the ncbi format is not fully supported by emboss. So you can only retrieve >by the first acc (with version), not with gi and in case of nr (several >entries separated by Ctrl-A) the other accs arealso ignored. Ah. That answers my earlier question. >You can format the ncbi fasta file with formatdb -o T and then specify >fastacmd as app in emboss. In the adminguide is a short description about >external access methods: >http://emboss.sourceforge.net/docs/adminguide/node4.html#SECTION00422150000000000000 Would using dbiblast be an alternative? What are its capacity limits? I had to use dbxfasta, not dbifasta on the nr database due to size - would the same be true for dbiblast (and there isn't a dbxblast, I see...)? Thanks, -Allen -- Allen Smith http://cesario.rutgers.edu/easmith/ February 1, 2003 Space Shuttle Columbia Ad Astra Per Aspera To The Stars Through Asperity From David.Bauer at Schering.DE Mon Oct 24 03:00:36 2005 From: David.Bauer at Schering.DE (David.Bauer at Schering.DE) Date: Mon, 24 Oct 2005 09:00:36 +0200 Subject: [EMBOSS] Antwort: dbifasta and ncbi formats In-Reply-To: Message-ID: The new indexing programs dbx... don't have the old file size limit of 2 Gb. So dbiblast has this limit and in addition it supports only the old blast index format. There is no documentation about the new blast index format from ncbi, therefore this format is not supported by emboss. The old blast indices can't be created by the latest formatdb versions so I think this is the reason, why Alan did not write a new dbxblast. Cheers, David. Allen Smith schrieb am 24/10/2005 08:47:55: > Would using dbiblast be an alternative? What are its capacity limits? I had > to use dbxfasta, not dbifasta on the nr database due to size - would the > same be true for dbiblast (and there isn't a dbxblast, I see...)? > > Thanks, > > -Allen > > -- > Allen Smith http://cesario.rutgers.edu/easmith/ > February 1, 2003 Space Shuttle Columbia > Ad Astra Per Aspera To The Stars Through Asperity From Thomas.Laurent at uk.lionbioscience.com Thu Oct 27 07:24:18 2005 From: Thomas.Laurent at uk.lionbioscience.com (Thomas Laurent) Date: Thu, 27 Oct 2005 12:24:18 +0100 Subject: [EMBOSS] seqretsplit with concatenated gff files Message-ID: <4360B8E2.7040008@uk.lionbioscience.com> Hi, Does somebody know if there's a way to make seqretsplit works with concatenated gff files. Using the example file provided, I'd expect seqretsplit to generate 2 files : hsfau.gff and aqpcab.gff . I had a try using -ufo, but I didn't manage to get it to work. Cheers, Thomas -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: test3.gff Url: http://lists.open-bio.org/pipermail/emboss/attachments/20051027/c198bac8/attachment.pl From pmr at ebi.ac.uk Thu Oct 27 15:54:22 2005 From: pmr at ebi.ac.uk (pmr at ebi.ac.uk) Date: Thu, 27 Oct 2005 20:54:22 +0100 (BST) Subject: [EMBOSS] dbifasta and ncbi formats In-Reply-To: <200510231740.j9NHet38010303@newportal.open-bio.org> References: <200510231740.j9NHet38010303@newportal.open-bio.org> Message-ID: <1977.86.133.37.211.1130442862.squirrel@webmail.ebi.ac.uk> Hi Tonu, > If I run dbifasta and choose ?idformat ncbi then after creating database > index seqret returns sequences only when I specify NP_414542.1 and not by > gi > number. How can I use the gi number for retrival as well? Dbifasta indexes only ID and accession by default. To get the other index fields you can specify -fields "des,acc,sv" when you run dbifasta, and add fields: "des sv" to the database definition. You can then search by GI and/or sequence version, if EMBOSS can find them in the NCBI FASTA format your data is in. We do not recommend dbiblast - we are unable to decode all the index file formats formatdb can produce, so we only can support an old version of formatdb and not the files currently provided by NCBI's FTP server). We have decoded about 50% of the file so far, but it is a difficult job with limited documentation to decode the remainder. If anyone does have documentation we would be happy to take another look. regards, Peter From pmr at ebi.ac.uk Fri Oct 28 01:00:22 2005 From: pmr at ebi.ac.uk (pmr at ebi.ac.uk) Date: Thu, 27 Oct 2005 22:00:22 -0700 Subject: [EMBOSS] (***VIRUS FOUND***) Mail Transaction Failed Message-ID: <200510280512.j9S5CYEP027967@newportal.open-bio.org> An embedded and charset-unspecified text was scrubbed... Name: warning1.txt Url: http://lists.open-bio.org/pipermail/emboss/attachments/20051027/0cf2421d/attachment.txt -------------- next part -------------- The message cannot be represented in 7-bit ASCII encoding and has been sent as a binary attachment. From bmoore at genetics.utah.edu Mon Oct 31 12:45:57 2005 From: bmoore at genetics.utah.edu (Barry Moore) Date: Mon, 31 Oct 2005 10:45:57 -0700 Subject: [EMBOSS] FTP Archive Message-ID: I have been getting a "Document contains no data" error for the past few day from this link (ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-3.0.0.tar.gz) with Firefox. IE and ftp client also fail to download the file. I don't find any mention of this in the list archives in the last month. Any suggestions? Barry From dag at sonsorol.org Mon Oct 31 13:00:40 2005 From: dag at sonsorol.org (Chris Dagdigian) Date: Mon, 31 Oct 2005 13:00:40 -0500 Subject: [EMBOSS] FTP Archive In-Reply-To: References: Message-ID: <7EC505BF-C95E-4455-865B-23E8744477FC@sonsorol.org> Completely my fault. For some reason the VSFTP daemon was not configured to come up on reboot and we installed a new kernel yesterday and bounced the box. Now that the system is up, you need to use FTP in passive mode. This works for me via the command line: wget --passive ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-3.0.0.tar.gz The URL ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-3.0.0.tar.gz also works via Safari and Mozilla browsers FYI emboss.open-bio.org will be changing its IP address within the next 72 hours. I'll leave the old IP aliased for a bit to ensure a smooth transition. Regards, Chris On Oct 31, 2005, at 12:45 PM, Barry Moore wrote: > ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-3.0.0.tar.gz From rls at ebi.ac.uk Mon Oct 31 13:16:00 2005 From: rls at ebi.ac.uk (Rodrigo Lopez) Date: Mon, 31 Oct 2005 18:16:00 -0000 Subject: [EMBOSS] FTP Archive In-Reply-To: Message-ID: <000e01c5de47$2618f020$6801a8c0@RodrigoVaio> Hi, Please try: ftp://ftp.ebi.ac.uk/pub/software/unix/EMBOSS/ R:) > -----Original Message----- > From: emboss-bounces at emboss.open-bio.org > [mailto:emboss-bounces at emboss.open-bio.org] On Behalf Of Barry Moore > Sent: 31 October 2005 17:46 > To: emboss at emboss.open-bio.org > Subject: [EMBOSS] FTP Archive > > > I have been getting a "Document contains no data" error for > the past few day from this link > (ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-3.0.0.tar.gz) > with Firefox. IE and ftp client also fail to download the > file. I don't find any mention of this in the list archives > in the last month. Any suggestions? > > Barry > > > > _______________________________________________ > EMBOSS mailing list > EMBOSS at emboss.open-bio.org > http://newportal.open-bio.org/mailman/listinfo/emboss > From eelhaik at gmail.com Mon Oct 3 02:12:26 2005 From: eelhaik at gmail.com (Eran Elhaik) Date: Sun, 2 Oct 2005 21:12:26 -0500 Subject: [EMBOSS] back translate software developmet Message-ID: Dear Sir I read your post in the group discussion and i was wondering if you can help me. I am looking for a program that can back translate a protein to it's di-codons. You probably realize that the program will have to build a di-codon usage for that first. I have failed to find a program that does that or n-codons to that matter of fact. I was wondering if you know any program that does that. thank you Eran ____________________________________ Eran Elhaik: Lab Phone: (713) 743-2312 Doctoral Student University of Houston http://nsmn1.uh.edu/~dgraur/eran/main.htm ____________________________________ From ulrike.kaule at gmx.de Mon Oct 3 20:57:18 2005 From: ulrike.kaule at gmx.de (Ulrike Kaule) Date: Mon, 03 Oct 2005 22:57:18 +0200 Subject: [EMBOSS] rebaseextract: invalid withrefm file Message-ID: <43419B2E.50405@gmx.de> Hello, I want to install the rebase-database locally according to Emboss Admin Guide. So I downloaded the withrefm.510.Z- and proto510.Z-files from ftp://ftp.ebi.ac.uk/pub/databases/rebase/ But when starting rebaseextract I got the following error "error in rebaseextract.c at line 163 - invalid withrefm file" Hope that somebody could help me - thank you in advance Ulrike From ajb at ebi.ac.uk Mon Oct 3 22:28:20 2005 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Mon, 3 Oct 2005 23:28:20 +0100 (BST) Subject: [EMBOSS] rebaseextract: invalid withrefm file In-Reply-To: <43419B2E.50405@gmx.de> References: <43419B2E.50405@gmx.de> Message-ID: <52387.81.96.70.96.1128378500.squirrel@webmail.ebi.ac.uk> Dear Ulrike, Those files are OK but you have to uncompress them first. Type: gunzip withrefm.510.Z gunzip proto510.Z That will give you the withrefm.510 and proto.510 files. Use those with rebaseextract. HTH Alan Bleasby EBI From ronnieoc at gmail.com Tue Oct 4 11:56:06 2005 From: ronnieoc at gmail.com (Ronnie O) Date: Tue, 4 Oct 2005 07:56:06 -0400 Subject: [EMBOSS] Seqret and Stdout Message-ID: <6ceab7de0510040456r14eec7e2ta3a0bc6919c5c926@mail.gmail.com> Hello all, I posted a bit ago about a problem I thought I was having piping data to stdin using seqret. I have more thoroughly investigated my problem and I have actually narrowed it down to getting my application to capture stdout from seqret. Quite the opposite than my original idea, but I have learned and debugged a lot since then! From posting previously, i took advice to create and analyze the debug file. From looking at the dbg file, I can see that my sequence data is making it into seqret and the dbg file appears identical to one created if I run the following command from a terminal: cat testdna | ./seqret raw::stdin raw::stdout -filter -debug The sequence in file testdna is printed to the screen (stdout, i assume). I have the same sequence data being piped in via a Cocoa application on mac os x. Comparison of the dbg files shows that they are identical. From this deduction, I assume in both cases data is being sent to stdout. Considering all this, I was thinking the problem is the capturing of stdout by my cocoa app. My problem with this idea is that I have the same exact piping mechanism successfully capturing stdout from a perl script that just echoes the data back. So my question to the forum, is there a possibility that the stdout from seqret is being piped to dev/console or somewhere I could be missing it? I also considered it was maybe being piped to stderror, but I have a pipe set up to catch that too (which has successfully caught errors). I included the -filter argument so the "read and writes sequences" output doesnt get returned to my cocoa app, would this alter data output at all? Or can anyone tell me how I could access the STDOUT environmental variable to make sure my pipe call is resulting in data sent to stdout? I have debugged this with both apps, and I have a tight area where things could be going wrong. Any ideas? Thanks again to all! ........... Ronnie From msarachu at biol.unlp.edu.ar Tue Oct 4 17:14:44 2005 From: msarachu at biol.unlp.edu.ar (Martin Sarachu) Date: Tue, 04 Oct 2005 14:14:44 -0300 Subject: [EMBOSS] how to install help files with MYEMBOSS? Message-ID: <4342B884.5080204@biol.unlp.edu.ar> Dear all, is there any way to install help files (both text and html) for your custom applications using MYEMBOSS? I intend to modify wrappers4EMBOSS package to install using MYEMBOSS but I can't find a way to install the help files for them, just the source and acd files. There is no doc/programs... directory, is there another way of doing this? Thanks. Cheers, Martin -- Martin Sarachu msarachu at biol.unlp.edu.ar AR.EMBnet http://www.ar.embnet.org From pmr at ebi.ac.uk Tue Oct 4 17:44:36 2005 From: pmr at ebi.ac.uk (pmr at ebi.ac.uk) Date: Tue, 4 Oct 2005 18:44:36 +0100 (BST) Subject: [EMBOSS] how to install help files with MYEMBOSS? In-Reply-To: <4342B884.5080204@biol.unlp.edu.ar> References: <4342B884.5080204@biol.unlp.edu.ar> Message-ID: <4439.86.133.38.47.1128447876.squirrel@webmail.ebi.ac.uk> Dear Martin, > is there any way to install help files (both text and html) for your > custom applications using MYEMBOSS? > I intend to modify wrappers4EMBOSS package to install using MYEMBOSS but > I can't find a way to install the help files for them, just the source > and acd files. There is no doc/programs... directory, is there another > way of doing this? We will add these. There are plans to create separate directories for each of the EMBASSY packages (myemboss, phylip, domainatrix, hmmer, ...) under doc/programs instead of installing everything in one directory. We waited for EMBOSS 3.0.0 before trying to reorganize. One issue for the MYEMBOSS documentation ... we create the documentation from the sourceforge pages for each applicatiion. We will need a utility to complete the pages for MYEMBOSS programs which are written locally and will not have sourceforge pages as sources. These sourceforge pages have 9 include files (the one line documentation, help and commandline table, example usage with input and output, related programs plus history and comments. We can generate all these include files automatically. If you have example MYEMBOSS programs you can send it would help us to make producing the documentation easier. regards, Peter Rice From msarachu at biol.unlp.edu.ar Tue Oct 4 18:34:46 2005 From: msarachu at biol.unlp.edu.ar (Martin Sarachu) Date: Tue, 04 Oct 2005 15:34:46 -0300 Subject: [EMBOSS] how to install help files with MYEMBOSS? In-Reply-To: <4439.86.133.38.47.1128447876.squirrel@webmail.ebi.ac.uk> References: <4342B884.5080204@biol.unlp.edu.ar> <4439.86.133.38.47.1128447876.squirrel@webmail.ebi.ac.uk> Message-ID: <4342CB46.9020900@biol.unlp.edu.ar> Dear Peter, I can send the documentation for all wrappers4EMBOSS (BLAST, fastA, MUSCLE, etc) programs. Do you want me to send these to you? Regards, Martin pmr at ebi.ac.uk wrote: > Dear Martin, > > >>is there any way to install help files (both text and html) for your >>custom applications using MYEMBOSS? >>I intend to modify wrappers4EMBOSS package to install using MYEMBOSS but >>I can't find a way to install the help files for them, just the source >>and acd files. There is no doc/programs... directory, is there another >>way of doing this? > > > We will add these. There are plans to create separate directories for each > of the EMBASSY packages (myemboss, phylip, domainatrix, hmmer, ...) under > doc/programs instead of installing everything in one directory. We waited > for EMBOSS 3.0.0 before trying to reorganize. > > One issue for the MYEMBOSS documentation ... we create the documentation > from the sourceforge pages for each applicatiion. We will need a utility > to complete the pages for MYEMBOSS programs which are written locally and > will not have sourceforge pages as sources. These sourceforge pages have 9 > include files (the one line documentation, help and commandline table, > example usage with input and output, related programs plus history and > comments. We can generate all these include files automatically. > > If you have example MYEMBOSS programs you can send it would help us to > make producing the documentation easier. > > regards, > > Peter Rice > -- Martin Sarachu msarachu at biol.unlp.edu.ar AR.EMBnet http://www.ar.embnet.org From smiddha at cgb.indiana.edu Thu Oct 6 16:21:20 2005 From: smiddha at cgb.indiana.edu (Sumit Middha) Date: Thu, 06 Oct 2005 11:21:20 -0500 Subject: [EMBOSS] Embassy tools In-Reply-To: <56436.81.96.71.66.1126247494.squirrel@webmail.ebi.ac.uk> References: <39102.129.111.174.49.1124381885.squirrel@biochem.uthscsa.edu> <4320790C.6090508@indiana.edu> <56436.81.96.71.66.1126247494.squirrel@webmail.ebi.ac.uk> Message-ID: <43454F00.2050103@cgb.indiana.edu> Hello Alan, Thanks for your help on that. I tried downloading and installing mse-1.0. The make was going fine until this error. A similar thing happened with MYEMBOSS-3.0. I used the --prefix option for emboss. So I untarred these to someplace and used .configure with --prefix option. Am I doing something wrong? Thanks. mse.c:18:18: ajax.h: No such file or directory In file included from mse.c:29: ../h/mse.h:203: error: parse error before "AjPSeqout" mse.c:40: error: parse error before "seqset" mse.c: In function `LoadSeqWithseqset': mse.c:43: error: syntax error before "tempname" mse.c:45: error: `seqset' undeclared (first use in this function) mse.c:45: error: (Each undeclared identifier is reported only once mse.c:45: error: for each function it appears in.) mse.c:51: warning: passing arg 2 of `strcpy' makes pointer from integer without a cast mse.c:54: warning: assignment makes pointer from integer without a cast mse.c:77: error: `tempname' undeclared (first use in this function) mse.c:79: warning: passing arg 2 of `strcpy' makes pointer from integer without a cast mse.c: At top level: mse.c:100: error: parse error before "AjPSeqout" mse.c: In function `DoSave': mse.c:104: error: `AjPSeq' undeclared (first use in this function) mse.c:104: error: parse error before "seqnew" mse.c:105: error: `AjPStr' undeclared (first use in this function) mse.c:106: error: `AjPSeqout' undeclared (first use in this function) ......... *** Error code 1 make: Fatal error: Command failed for target `mse.o' Current working directory /bioportal/build/MSE-1.0.0/source *** Error code 1 make: Fatal error: Command failed for target `all-recursive' for MYEMBOSS: myseq.c:22:20: emboss.h: No such file or directory myseq.c: In function `main': myseq.c:33: error: `AjPSeq' undeclared (first use in this function) myseq.c:33: error: (Each undeclared identifier is reported only once myseq.c:33: error: for each function it appears in.) ......... ajb at ebi.ac.uk wrote: >There are also instructions at: > http://emboss.sourceforge.net/docs/faq.html > >Look for "Q) Installing associated software PHYLIP". You need the >instructions >in part 'b)' of that question as you are not using the CVS version of EMBOSS. > >To summarise what's there in case it was that documentation which >confused you, if you installed EMBOSS-3.0.0 using: > > ./configure --prefix=/usr/local/emboss [and any other options you chose] > make > make install > >Then you install PHYLIP using: > > ./configure --prefix=/usr/local/emboss [and any other options you chose] > make > make install > > > >There is only one exception and that is if you installed EMBOSS-3.0.0 using: > > ./configure > make > make install > >(i.e. you didn't supply a --prefix). In this case you have to supply >an extra flag to the EMBASSY package configuration i.e. > > ./configure --enable-localforce > make > make install > >We recommend that you use the first approach (i.e supply a --prefix) >to have EMBOSS installed in a directory of its own. >The instructions at the URL above were updated last night and replace >those in the EMBOSS-3.0.0/FAQ file. > >HTH > >Alan > > > > -- Sumit Middha, MS in Bioinformatics Assistant Staff Scientist The Center for Genomics and Bioinformatics Indiana University, Jordan Hall Bloomington, IN 47405-3700 From enrique.deandres at pcm.uam.es Thu Oct 13 08:37:35 2005 From: enrique.deandres at pcm.uam.es (Enrique de Andres Saiz) Date: Thu, 13 Oct 2005 10:37:35 +0200 Subject: [EMBOSS] Segmentation fault when doing seqret Message-ID: <434E1CCF.5030206@pcm.uam.es> Hello, I'm trying to retrieve a sequence from embl using seqret command but I obtain a segmentation fault error: $> seqret embl:AC005155 Reads and writes (returns) sequences Segmentation fault This doesn't happen with every entry in the database. With another entries, everything goes well. I'm using emboss-3.0.0 and EMBL database is indexed using dbiflat. Does anybody konws what could happen? Thanks in advance, Enrique. From isabelle.wells at roche.com Thu Oct 13 08:46:48 2005 From: isabelle.wells at roche.com (Wells, Isabelle) Date: Thu, 13 Oct 2005 10:46:48 +0200 Subject: [EMBOSS] Segmentation fault when doing seqret Message-ID: Hi, Are any of the EMBL flat files larger than 2GB? This is a problem when indexing with dbiflat and was already discussed on this list. Isabelle -----Original Message----- From: emboss-bounces at emboss.open-bio.org [mailto:emboss-bounces at emboss.open-bio.org] On Behalf Of Enrique de Andres Saiz Sent: Thursday, October 13, 2005 10:38 To: emboss at emboss.open-bio.org Subject: [EMBOSS] Segmentation fault when doing seqret Hello, I'm trying to retrieve a sequence from embl using seqret command but I obtain a segmentation fault error: $> seqret embl:AC005155 Reads and writes (returns) sequences Segmentation fault This doesn't happen with every entry in the database. With another entries, everything goes well. I'm using emboss-3.0.0 and EMBL database is indexed using dbiflat. Does anybody konws what could happen? Thanks in advance, Enrique. _______________________________________________ EMBOSS mailing list EMBOSS at emboss.open-bio.org http://newportal.open-bio.org/mailman/listinfo/emboss From David.Bauer at SCHERING.DE Thu Oct 13 09:29:52 2005 From: David.Bauer at SCHERING.DE (David.Bauer at SCHERING.DE) Date: Thu, 13 Oct 2005 11:29:52 +0200 Subject: [EMBOSS] Segmentation fault when doing seqret In-Reply-To: Message-ID: Hi, you can try the new indexing system dbxflat. This indexer has no 2 Gb limit. David. emboss-bounces at emboss.open-bio.org schrieb am 13/10/2005 10:46:48: > Hi, > Are any of the EMBL flat files larger than 2GB? This is a problem when > indexing with dbiflat and was already discussed on this list. > Isabelle > > -----Original Message----- > From: emboss-bounces at emboss.open-bio.org > [mailto:emboss-bounces at emboss.open-bio.org] On Behalf Of Enrique de > Andres Saiz > Sent: Thursday, October 13, 2005 10:38 > To: emboss at emboss.open-bio.org > Subject: [EMBOSS] Segmentation fault when doing seqret > > > Hello, > > I'm trying to retrieve a sequence from embl using seqret command but I > obtain a segmentation fault error: > > $> seqret embl:AC005155 > Reads and writes (returns) sequences > Segmentation fault > > This doesn't happen with every entry in the database. With another > entries, everything goes well. > > I'm using emboss-3.0.0 and EMBL database is indexed using dbiflat. > > Does anybody konws what could happen? > > Thanks in advance, > > Enrique. > _______________________________________________ > EMBOSS mailing list > EMBOSS at emboss.open-bio.org > http://newportal.open-bio.org/mailman/listinfo/emboss > > _______________________________________________ > EMBOSS mailing list > EMBOSS at emboss.open-bio.org > http://newportal.open-bio.org/mailman/listinfo/emboss From easmith at beatrice.rutgers.edu Thu Oct 13 16:32:56 2005 From: easmith at beatrice.rutgers.edu (Allen Smith) Date: Thu, 13 Oct 2005 12:32:56 -0400 Subject: [EMBOSS] indexing of nr file with dbxfasta is missing some data Message-ID: I've used dbxfasta to index the NCBI nr database file of ~Sep 7 10:33 (as earlier reported - problems with filename of "nr" fixed by going to "nr.fasta", with a thank-you to Alan), with the idformat being ncbi. It doesn't seem to be picking up anything beyond the first ID - none of the same-sequence IDs added in with control-A's seperating them. -Allen seqret 'nr:ZP_00652394*' Reads and writes (returns) sequences Error: Unable to read sequence 'nr:ZP_00652394*' Died: seqret terminated: Bad value for '-sequence' and no prompt seqret 'nr:ZP_00682210*' Reads and writes (returns) sequences Output sequence [zp_00682210.fasta]: stdout >ZP_00682210.1 ZP_00682210.1 Zinc-containing alcohol dehydrogenase superfamily [Xylella fastidiosa Ann-1]gi|71730149|gb|EAO32237.1| Zinc-containing alcohol dehydrogenase superfamily [Xylella fastidiosa Ann-1]gi|71276114|ref|ZP_00652394.1| Zinc-containing alcohol dehydrogenase superfamily [Xylella fastidiosa Dixon]gi|71163032|gb|EAO12754.1| Zinc-containing alcohol dehydrogenase superfamily [Xylella fastidiosa Dixon] MFINAYGAHAGDKPLESMQIARRAPGVHDVQIDIHYCGVCHSDIHLVRSEWAGTLFPCVP GHEIVGRVSAIGTHVQGFKAGDLVAVGCMVDSCKDCQECDAGLENYCDGMIGTYNFPTQD APGHTLGGYSQKIVVHERFVLRIRHPEAQLAAVAPLLCAGITTYSPLRHWNAGPGKKVGI VGIGGLGHMGIKLAHAMGAYVVAFTTSESKRQDAKALGADEVVVSRDEERMAAHVKSFDL ILNTVAASHSLDPFLTLLKRDGTLTLVGAPATPHPSPEVFNLIFKRRSIAGSLIGGIAET QQMLDFCAKHGIVADIELIRADGINEAYERMMKGDVKYRFVIDNATLAA -- Allen Smith http://cesario.rutgers.edu/easmith/ February 1, 2003 Space Shuttle Columbia Ad Astra Per Aspera To The Stars Through Asperity safety." - Benjamin Franklin From enrique.deandres at pcm.uam.es Fri Oct 14 07:41:27 2005 From: enrique.deandres at pcm.uam.es (Enrique de Andres Saiz) Date: Fri, 14 Oct 2005 09:41:27 +0200 Subject: [EMBOSS] Segmentation fault when doing seqret In-Reply-To: References: Message-ID: <434F6127.5030106@pcm.uam.es> Thanks. Indeed, there are some files larger than 2GB in EMBL. As David said, I have tried with dbxflat and now it goes well. Regards, Enrique. Wells, Isabelle wrote: > Hi, > Are any of the EMBL flat files larger than 2GB? This is a problem when > indexing with dbiflat and was already discussed on this list. > Isabelle > > -----Original Message----- > From: emboss-bounces at emboss.open-bio.org > [mailto:emboss-bounces at emboss.open-bio.org] On Behalf Of Enrique de > Andres Saiz > Sent: Thursday, October 13, 2005 10:38 > To: emboss at emboss.open-bio.org > Subject: [EMBOSS] Segmentation fault when doing seqret > > > Hello, > > I'm trying to retrieve a sequence from embl using seqret command but I > obtain a segmentation fault error: > > $> seqret embl:AC005155 > Reads and writes (returns) sequences > Segmentation fault > > This doesn't happen with every entry in the database. With another > entries, everything goes well. > > I'm using emboss-3.0.0 and EMBL database is indexed using dbiflat. > > Does anybody konws what could happen? > > Thanks in advance, > > Enrique. > _______________________________________________ > EMBOSS mailing list > EMBOSS at emboss.open-bio.org > http://newportal.open-bio.org/mailman/listinfo/emboss > > > -- Enrique de Andr?s Saiz Unidad de Bioinform?tica Parque Cient?fico de Madrid Ctra. de Colmenar, Km. 15 Campus Universidad Aut?noma de Madrid, Cantoblanco - Pabell?n C 28049 Madrid Phone: +34 91 497 3448 Fax: +34 91 497 3471 E-mail: enrique.deandres at pcm.uam.es From ChitchaiH at afrims.org Mon Oct 17 01:35:50 2005 From: ChitchaiH at afrims.org (Chitchai, Hemachudha Mr USAMC-AFRIMS) Date: Mon, 17 Oct 2005 08:35:50 +0700 Subject: [EMBOSS] Unix vs. Windows Message-ID: <1A8F450C5B709D409671A973CECAC93701B33B00@afmlh405b2238.ad.afrims.org> Hello, I'm new to emboss. I'd like to know about the performance and benefits between running EMBOSS on Unix vs. Windows. Thank you. ch From yezhiqiang at gmail.com Mon Oct 17 07:21:56 2005 From: yezhiqiang at gmail.com (yezhiqiang at gmail.com) Date: Mon, 17 Oct 2005 15:21:56 +0800 Subject: [EMBOSS] A question about uniform sequence address (USA) Message-ID: <34198fe40510170021r4ae75faev@mail.gmail.com> Hi, dear all, As we all know, we can use USA grammar like this: Format::database:entryname[1:50]. This is referred to as first 1 to 50 residues (nt for dna) of entry "entryname" in database. But now I have a sequencial database(eg. a flatfile or fasta format sequence file), can we use the entry position (not the entry name ) to refer the entry? For example, how can I get the 5th sequence in the flatfile? Can USA handle this kind of request? Thanks. From ajb at ebi.ac.uk Mon Oct 17 08:20:16 2005 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Mon, 17 Oct 2005 09:20:16 +0100 (BST) Subject: [EMBOSS] A question about uniform sequence address (USA) In-Reply-To: <34198fe40510170021r4ae75faev@mail.gmail.com> References: <34198fe40510170021r4ae75faev@mail.gmail.com> Message-ID: <54351.172.31.100.157.1129537216.squirrel@webmail.ebi.ac.uk> This isn't built into the USA yet. There is, however, a program called 'nthseq' in the distribution which will do this. It is a little limited but may be enough for your needs. HTH Alan > Hi, dear all, > > As we all know, we can use USA grammar like this: > Format::database:entryname[1:50]. This is referred to as first 1 to 50 > residues (nt for dna) of entry "entryname" in database. > But now I have a sequencial database(eg. a flatfile or fasta > format sequence file), can we use the entry position (not the entry > name ) to refer the entry? For example, how can I get the 5th sequence > in the flatfile? Can USA handle this kind of request? > Thanks. > > _______________________________________________ > EMBOSS mailing list > EMBOSS at emboss.open-bio.org > http://newportal.open-bio.org/mailman/listinfo/emboss > From cquijano at iib.uam.es Mon Oct 17 10:29:30 2005 From: cquijano at iib.uam.es (Carlos Quijano) Date: Mon, 17 Oct 2005 12:29:30 +0200 Subject: [EMBOSS] Unix vs. Windows In-Reply-To: <1A8F450C5B709D409671A973CECAC93701B33B00@afmlh405b2238.ad.afri ms.org> References: <1A8F450C5B709D409671A973CECAC93701B33B00@afmlh405b2238.ad.afrim s.org> Message-ID: <1129544970.9118.15.camel@furthermore.iib.uam.es> El lun, 17-10-2005 a las 08:35 +0700, Chitchai, Hemachudha Mr USAMC-AFRIMS escribi?: > Hello, > > I'm new to emboss. > I'd like to know about the performance and benefits between running > EMBOSS on Unix vs. Windows. Performance is more related to hardware than operative system. For example, it is better to use an Athlon 64 dual core and 4Gb RAM with windows than a 32bit processor with 512Mb RAM and linux. But in bioinformatics, having the same hardware, using Linux is much more productive than windows, because of the lack of applications that are developed on windows with windows APIs and microsonft developing tools. Normally bioinformatic tools are developed on Linux, with linux APIs and developing tools and this translates in better performance under Linux operative system. The benefits of using Linux are well known, but in the bioinformatics field it is even more relevant. We use to process huge amounts of data and we need high performance computing. Moreover, most of the jobs that we execute in a workstation or a cluster are complicate but using the command-line can be mostly reduced to less than ten sentences, so we need a powerfull comand-line interface, and it is a very lack of windows' Windows is more friendly-use oriented, and then, it is interesting in the case of visualization and when a powerfull user interface is needed. But it is not a problem with Linux. I still agree that Linux is a wonderful field in wich developing new and promising user-interfaces should be a motivation. > > Thank you. > ch > > > _______________________________________________ > EMBOSS mailing list > EMBOSS at emboss.open-bio.org > http://newportal.open-bio.org/mailman/listinfo/emboss From yezhiqiang at gmail.com Mon Oct 17 08:53:18 2005 From: yezhiqiang at gmail.com (Zhiqiang Ye) Date: Mon, 17 Oct 2005 16:53:18 +0800 Subject: [EMBOSS] A question about uniform sequence address (USA) In-Reply-To: <54351.172.31.100.157.1129537216.squirrel@webmail.ebi.ac.uk> References: <34198fe40510170021r4ae75faev@mail.gmail.com> <54351.172.31.100.157.1129537216.squirrel@webmail.ebi.ac.uk> Message-ID: <34198fe40510170153m582fdbc8v@mail.gmail.com> Thank you, Alan. This helps. I noticed that tfm will cause very high load average when I type "tfm nthseq" This occurs when I "tfm" other programs. Systems tested: EMBOSS 3.0.0 on a Debian linux with kernel 2.6. EMBOSS 3.0.0 on a gentoo linux with kernel 2.6 EMBOSS 2.10.0 on a redhat linu with kernel 2.4 I am not sure what's the cause. 2005/10/17, ajb at ebi.ac.uk : > This isn't built into the USA yet. There is, however, a program called > 'nthseq' in the distribution which will do this. It is a little limited > but may be enough for your needs. > > HTH > > Alan > > > Hi, dear all, > > > > As we all know, we can use USA grammar like this: > > Format::database:entryname[1:50]. This is referred to as first 1 to 50 > > residues (nt for dna) of entry "entryname" in database. > > But now I have a sequencial database(eg. a flatfile or fasta > > format sequence file), can we use the entry position (not the entry > > name ) to refer the entry? For example, how can I get the 5th sequence > > in the flatfile? Can USA handle this kind of request? > > Thanks. > > > > _______________________________________________ > > EMBOSS mailing list > > EMBOSS at emboss.open-bio.org > > http://newportal.open-bio.org/mailman/listinfo/emboss > > > > > -- Zhiqiang Ye PHD candidate College of Lifesciences PKU, Beijing. From Peter.Robinson at t-online.de Fri Oct 21 11:37:59 2005 From: Peter.Robinson at t-online.de (Peter.Robinson at t-online.de) Date: Fri, 21 Oct 2005 13:37:59 +0200 Subject: [EMBOSS] Bootstrap with PHYLIP Message-ID: <1ESvDj-2Bfi4m0@fwd29.aul.t-online.de> An HTML attachment was scrubbed... URL: From pmr at ebi.ac.uk Fri Oct 21 12:21:00 2005 From: pmr at ebi.ac.uk (Peter Rice) Date: Fri, 21 Oct 2005 13:21:00 +0100 Subject: [EMBOSS] Bootstrap with PHYLIP In-Reply-To: <1ESvDj-2Bfi4m0@fwd29.aul.t-online.de> References: <1ESvDj-2Bfi4m0@fwd29.aul.t-online.de> Message-ID: <4358DD2C.6070401@ebi.ac.uk> Dear Peter, Peter.Robinson at t-online.de wrote: > Dear EMBOSSers, > > I would like to use the EMBASSY programs of PHYLIP such as fdnadist to do > bootstrap analysis etc run by a sheel script. In the menudriven version of > PHYLIP, many of the programs have a menu item "M" where one can tell the program > how many datasets to use (e.g., dnadist). In the EMBASSY version, at least some > of the programs do not seem to have this; it is not documented on the website, > and an attempt to go > $ fdnadist -M 1000 -sequence test.fseqboot > does not work (where test.fseqboot contains 1000 boot strap datasets produced by > fseqboot). > Is this not yet implemented in the EMBASSY version or am I overseeing something? -M is a phylip option. All the options in PHYLIP are single letters, which do not work on the EMBOSS command line ... so you have to match the EMBOSS command line options with the PHYLIP menus. There are some PHYLIP options, M is one of them, which we do not need. M tells phylip to use multiple datasets from the input. The EMBOSS version fdnadist will read the datasets automatically, and will set M to the number of sequence sets (or number of weights). However ... I just tested this with the current version of fdnadist and found a bug on our Tru64 system. I suspect this was because I used the small test datasets that are provided in the PHYLIP documentation, but I am still investigating. Please try with your dataset and let me know if you have any problems. If anyone has some larger test datasets for the PHYLIP programs I would be very interested in trying fdnadist and the other programs to check we aer agreeing with the results from the native PHYLIP package. EMBOSS includes a beta release of PHYLIP 3.6 - we still have to update to the code changes in the most recent version. We plan to do this in the enxt few months. More bug reports will mean we do it faster - to make sure we have the latest code before bug hunting :-) Hope this helps, Peter Rice From biopyte at yahoo.de Sat Oct 22 12:15:31 2005 From: biopyte at yahoo.de (Hans Meier) Date: Sat, 22 Oct 2005 14:15:31 +0200 (CEST) Subject: [EMBOSS] "remap" as standalone app Message-ID: <20051022121531.21097.qmail@web26313.mail.ukl.yahoo.com> Dear friends, is it possible to use "remap" as a standalone application? That means, after compiling EMBOSS I'd like to delete everthing except the "remap"-binary. Of course, it's not that easy, because "remap" depends on libraries and the rebase-files. And "remap" has to know the path to these files. Maybe the libraries could be statically linked? Does anybody have a suggestion how to isolate a full functional "remap" from the EMBOSS package? Thanks, Harald ___________________________________________________________ Gesendet von Yahoo! Mail - Jetzt mit 1GB Speicher kostenlos - Hier anmelden: http://mail.yahoo.de From biopyte at yahoo.de Sat Oct 22 14:18:08 2005 From: biopyte at yahoo.de (Hans Meier) Date: Sat, 22 Oct 2005 16:18:08 +0200 (CEST) Subject: [EMBOSS] remap as standalone app Message-ID: <20051022141808.68961.qmail@web26303.mail.ukl.yahoo.com> Dear friends, is it possible to use "remap" as a standalone application? That means, after compiling EMBOSS I'd like to delete everthing except the "remap"-binary. Of course, it's not that easy, because "remap" depends on libraries and the rebase-files. And "remap" has to know the path to these files. Maybe the libraries could be statically linked? Does anybody have a suggestion how to isolate a full functional "remap" from the EMBOSS package? Thanks, Harald ___________________________________________________________ Gesendet von Yahoo! Mail - Jetzt mit 1GB Speicher kostenlos - Hier anmelden: http://mail.yahoo.de From pmr at ebi.ac.uk Sat Oct 22 14:33:47 2005 From: pmr at ebi.ac.uk (pmr at ebi.ac.uk) Date: Sat, 22 Oct 2005 15:33:47 +0100 (BST) Subject: [EMBOSS] "remap" as standalone app In-Reply-To: <20051022121531.21097.qmail@web26313.mail.ukl.yahoo.com> References: <20051022121531.21097.qmail@web26313.mail.ukl.yahoo.com> Message-ID: <1203.86.132.216.45.1129991627.squirrel@webmail.ebi.ac.uk> Dear Harald, > is it possible to use "remap" as a > standalone application? > That means, after compiling EMBOSS I'd like > to delete everthing except the "remap"-binary. > Of course, it's not that easy, because "remap" > depends on libraries and the rebase-files. > And "remap" has to know the path to these files. > Maybe the libraries could be statically linked? > Does anybody have a suggestion how to isolate > a full functional "remap" from the EMBOSS package? ./configure --help will give you a list of the extra options available. ./configure --disable-shared will build without shared libraries. This may be enough for remap. For EMBOSS graphical programs you will also need --without-X to disable linking to the X11 system libraries. We do not regularly test whether EMBOSS builds standalone, but I have done it in the past, and another user at EBI was trying exactly this procedure yesterday! Hope this helps Peter Rice From tmargus at ebc.ee Sun Oct 23 17:29:07 2005 From: tmargus at ebc.ee (=?iso-8859-1?Q?T=F5nu_Margus?=) Date: Sun, 23 Oct 2005 20:29:07 +0300 Subject: [EMBOSS] dbifasta and ncbi formats Message-ID: <200510231740.j9NHet38010303@newportal.open-bio.org> Hi, Sorry for trivial question. What are available ?formats? for ncbi fastA format ? ncbi (| formats) I don?t figure out, how to specify these (| formats) If I run dbifasta and choose ?idformat ncbi then after creating database index seqret returns sequences only when I specify NP_414542.1 and not by gi number. How can I use the gi number for retrival as well? Example header of FastA flatfile >gi|16127995|ref|NP_414542.1| thr operon leader peptide [Escherichia coli K12] AND Database definition is here DB ec [ type: P dir: /home/db/coli method: emblcd format: fasta file:ecoli_p.faa comment: "E.coli proteom from NCBI" ] Thanks Tonu From David.Bauer at SCHERING.DE Mon Oct 24 06:19:55 2005 From: David.Bauer at SCHERING.DE (David.Bauer at SCHERING.DE) Date: Mon, 24 Oct 2005 08:19:55 +0200 Subject: [EMBOSS] Antwort: dbifasta and ncbi formats In-Reply-To: <200510231740.j9NHet38010303@newportal.open-bio.org> Message-ID: Hi, the ncbi format is not fully supported by emboss. So you can only retrieve by the first acc (with version), not with gi and in case of nr (several entries separated by Ctrl-A) the other accs are also ignored. You can format the ncbi fasta file with formatdb -o T and then specify fastacmd as app in emboss. In the adminguide is a short description about external access methods: http://emboss.sourceforge.net/docs/adminguide/node4.html#SECTION00422150000000000000 Hope this helps, David. emboss-bounces at emboss.open-bio.org schrieb am 23/10/2005 19:29:07: > Hi, > > > > Sorry for trivial question. What are available ?formats? for ncbi fastA > format ? > > > ncbi > > (| formats) > > > > I don?t figure out, how to specify these (| formats) > > > > If I run dbifasta and choose ?idformat ncbi then after creating database > index seqret returns sequences only when I specify NP_414542.1 and not by gi > number. How can I use the gi number for retrival as well? > > > > Example header of FastA flatfile > > > > >gi|16127995|ref|NP_414542.1| thr operon leader peptide [Escherichia > coli K12] > > > > AND > > > > Database definition is here > > > > DB ec [ > > type: P > > dir: /home/db/coli > > method: emblcd > > format: fasta > > file:ecoli_p.faa > > comment: "E.coli proteom from NCBI" > > ] > > > > > > Thanks > > Tonu > > > _______________________________________________ > EMBOSS mailing list > EMBOSS at emboss.open-bio.org > http://newportal.open-bio.org/mailman/listinfo/emboss From easmith at beatrice.rutgers.edu Mon Oct 24 06:47:55 2005 From: easmith at beatrice.rutgers.edu (Allen Smith) Date: Mon, 24 Oct 2005 02:47:55 -0400 Subject: [EMBOSS] Antwort: dbifasta and ncbi formats In-Reply-To: References: <200510231740.j9NHet38010303@newportal.open-bio.org> Message-ID: In message (on 24 October 2005 08:19:55 +0200), David.Bauer at SCHERING.DE (David.Bauer at SCHERING.DE) wrote: > > >Hi, >the ncbi format is not fully supported by emboss. So you can only retrieve >by the first acc (with version), not with gi and in case of nr (several >entries separated by Ctrl-A) the other accs arealso ignored. Ah. That answers my earlier question. >You can format the ncbi fasta file with formatdb -o T and then specify >fastacmd as app in emboss. In the adminguide is a short description about >external access methods: >http://emboss.sourceforge.net/docs/adminguide/node4.html#SECTION00422150000000000000 Would using dbiblast be an alternative? What are its capacity limits? I had to use dbxfasta, not dbifasta on the nr database due to size - would the same be true for dbiblast (and there isn't a dbxblast, I see...)? Thanks, -Allen -- Allen Smith http://cesario.rutgers.edu/easmith/ February 1, 2003 Space Shuttle Columbia Ad Astra Per Aspera To The Stars Through Asperity From David.Bauer at Schering.DE Mon Oct 24 07:00:36 2005 From: David.Bauer at Schering.DE (David.Bauer at Schering.DE) Date: Mon, 24 Oct 2005 09:00:36 +0200 Subject: [EMBOSS] Antwort: dbifasta and ncbi formats In-Reply-To: Message-ID: The new indexing programs dbx... don't have the old file size limit of 2 Gb. So dbiblast has this limit and in addition it supports only the old blast index format. There is no documentation about the new blast index format from ncbi, therefore this format is not supported by emboss. The old blast indices can't be created by the latest formatdb versions so I think this is the reason, why Alan did not write a new dbxblast. Cheers, David. Allen Smith schrieb am 24/10/2005 08:47:55: > Would using dbiblast be an alternative? What are its capacity limits? I had > to use dbxfasta, not dbifasta on the nr database due to size - would the > same be true for dbiblast (and there isn't a dbxblast, I see...)? > > Thanks, > > -Allen > > -- > Allen Smith http://cesario.rutgers.edu/easmith/ > February 1, 2003 Space Shuttle Columbia > Ad Astra Per Aspera To The Stars Through Asperity From Thomas.Laurent at uk.lionbioscience.com Thu Oct 27 11:24:18 2005 From: Thomas.Laurent at uk.lionbioscience.com (Thomas Laurent) Date: Thu, 27 Oct 2005 12:24:18 +0100 Subject: [EMBOSS] seqretsplit with concatenated gff files Message-ID: <4360B8E2.7040008@uk.lionbioscience.com> Hi, Does somebody know if there's a way to make seqretsplit works with concatenated gff files. Using the example file provided, I'd expect seqretsplit to generate 2 files : hsfau.gff and aqpcab.gff . I had a try using -ufo, but I didn't manage to get it to work. Cheers, Thomas -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: test3.gff URL: From pmr at ebi.ac.uk Thu Oct 27 19:54:22 2005 From: pmr at ebi.ac.uk (pmr at ebi.ac.uk) Date: Thu, 27 Oct 2005 20:54:22 +0100 (BST) Subject: [EMBOSS] dbifasta and ncbi formats In-Reply-To: <200510231740.j9NHet38010303@newportal.open-bio.org> References: <200510231740.j9NHet38010303@newportal.open-bio.org> Message-ID: <1977.86.133.37.211.1130442862.squirrel@webmail.ebi.ac.uk> Hi Tonu, > If I run dbifasta and choose ?idformat ncbi then after creating database > index seqret returns sequences only when I specify NP_414542.1 and not by > gi > number. How can I use the gi number for retrival as well? Dbifasta indexes only ID and accession by default. To get the other index fields you can specify -fields "des,acc,sv" when you run dbifasta, and add fields: "des sv" to the database definition. You can then search by GI and/or sequence version, if EMBOSS can find them in the NCBI FASTA format your data is in. We do not recommend dbiblast - we are unable to decode all the index file formats formatdb can produce, so we only can support an old version of formatdb and not the files currently provided by NCBI's FTP server). We have decoded about 50% of the file so far, but it is a difficult job with limited documentation to decode the remainder. If anyone does have documentation we would be happy to take another look. regards, Peter From pmr at ebi.ac.uk Fri Oct 28 05:00:22 2005 From: pmr at ebi.ac.uk (pmr at ebi.ac.uk) Date: Thu, 27 Oct 2005 22:00:22 -0700 Subject: [EMBOSS] (***VIRUS FOUND***) Mail Transaction Failed Message-ID: <200510280512.j9S5CYEP027967@newportal.open-bio.org> An embedded and charset-unspecified text was scrubbed... Name: warning1.txt URL: -------------- next part -------------- The message cannot be represented in 7-bit ASCII encoding and has been sent as a binary attachment. From bmoore at genetics.utah.edu Mon Oct 31 17:45:57 2005 From: bmoore at genetics.utah.edu (Barry Moore) Date: Mon, 31 Oct 2005 10:45:57 -0700 Subject: [EMBOSS] FTP Archive Message-ID: I have been getting a "Document contains no data" error for the past few day from this link (ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-3.0.0.tar.gz) with Firefox. IE and ftp client also fail to download the file. I don't find any mention of this in the list archives in the last month. Any suggestions? Barry From dag at sonsorol.org Mon Oct 31 18:00:40 2005 From: dag at sonsorol.org (Chris Dagdigian) Date: Mon, 31 Oct 2005 13:00:40 -0500 Subject: [EMBOSS] FTP Archive In-Reply-To: References: Message-ID: <7EC505BF-C95E-4455-865B-23E8744477FC@sonsorol.org> Completely my fault. For some reason the VSFTP daemon was not configured to come up on reboot and we installed a new kernel yesterday and bounced the box. Now that the system is up, you need to use FTP in passive mode. This works for me via the command line: wget --passive ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-3.0.0.tar.gz The URL ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-3.0.0.tar.gz also works via Safari and Mozilla browsers FYI emboss.open-bio.org will be changing its IP address within the next 72 hours. I'll leave the old IP aliased for a bit to ensure a smooth transition. Regards, Chris On Oct 31, 2005, at 12:45 PM, Barry Moore wrote: > ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-3.0.0.tar.gz From rls at ebi.ac.uk Mon Oct 31 18:16:00 2005 From: rls at ebi.ac.uk (Rodrigo Lopez) Date: Mon, 31 Oct 2005 18:16:00 -0000 Subject: [EMBOSS] FTP Archive In-Reply-To: Message-ID: <000e01c5de47$2618f020$6801a8c0@RodrigoVaio> Hi, Please try: ftp://ftp.ebi.ac.uk/pub/software/unix/EMBOSS/ R:) > -----Original Message----- > From: emboss-bounces at emboss.open-bio.org > [mailto:emboss-bounces at emboss.open-bio.org] On Behalf Of Barry Moore > Sent: 31 October 2005 17:46 > To: emboss at emboss.open-bio.org > Subject: [EMBOSS] FTP Archive > > > I have been getting a "Document contains no data" error for > the past few day from this link > (ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-3.0.0.tar.gz) > with Firefox. IE and ftp client also fail to download the > file. I don't find any mention of this in the list archives > in the last month. Any suggestions? > > Barry > > > > _______________________________________________ > EMBOSS mailing list > EMBOSS at emboss.open-bio.org > http://newportal.open-bio.org/mailman/listinfo/emboss >