From ajb at ebi.ac.uk Thu Aug 11 09:20:31 2011 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Thu, 11 Aug 2011 14:20:31 +0100 (BST) Subject: [EMBOSS] EMBOSS and mEMBOSS bug-fixes for 6.4.0 released Message-ID: <53896.82.26.12.214.1313068831.squirrel@imap04.ebi.ac.uk> New bug-fix files are available for EMBOSS-6.4.0 and, for Windows users, a new version of mEMBOSS is available. The bugs fixed are appended for easy reference. 1) UNIX As usual, the most convenient way of applying the bug-fixes should be to apply the patch file: ftp://emboss.open-bio.org/pub/EMBOSS/fixes/patches/patch-1-11.gz to a freshly extracted copy of the EMBOSS-6.4.0.tar.gz source code and recompiling/installing. (see ftp://emboss.open-bio.org/pub/EMBOSS/fixes/patches/README.patch for instructions on using 'patch'). Alternatively, you can individually copy the patched files from the ftp://emboss.open-bio.org/pub/EMBOSS/fixes/ directory if your system does not support 'patch'. 2) mEMBOSS The new version incorporates all the bug-fixes listed below. Uninstall your previous mEMBOSS installation and download and install the new setup file from: ftp://emboss.open-bio.org/pub/EMBOSS/windows/mEMBOSS-6.4.0.2-setup.exe Alan ----------------------------------------------------------------------- Fix 1. EMBOSS-6.4.0/emboss/dbiflat.c EMBOSS-6.4.0/emboss/dbxflat.c 10 Aug 2011: The SwissProt description line format includes additional tags which interfere with the EMBL parser used in previous releases. The fix replaces this with a SwissProt parser that strips out the extra tags. After patching the release, any existing SwissProt description index files should be reindexed. Other indexes are unchanged. Fix 2. EMBOSS-6.4.0/ajax/core/ajquery.c 10 Aug 2011: For databases with more than one valid format (examples include the EBI dbfetch server) this fix allows the format to be specified with a qualifier on the command line. In the original release, only a format in the query string was used. Fix 3. EMBOSS-6.4.0/ajax/core/ajfeatread.c 10 Aug 2011: When parsing GFF3 format input, long feature tags (for example extremely long translations) exceeded limits in regular expression parsing. This fix decouples testing for escaped quotes from the main task of finding quoted strings. Fix 4. EMBOSS-6.4.0/emboss/data/Etcode.dat 10 Aug 2001: The local data file used by application tcode had a missing parameter line. Fix 5. EMBOSS-6.4.0/ajax/core/ajrange.c 10 Aug 2011: When sequence ranges (and possible highlighting for showalign) were in a list file, the parser overwrote string values. Fix 5. EMBOSS-6.4.0/ajax/core/ajseqabi.c 10 Aug 2011: Sample names in ABI format files were stored in incompletely defined strings. This fix corrects the string object. The sample name is also used as the sequence name. Fix 6. EMBOSS-6.4.0/emboss/dbxresource.c 10 Aug 2011: A future change to the format of Data Resource Catalogue entries in DRCAT.dat requires an update to the parsing of category lines. The current version is not affected. Fix 7. EMBOSS-6.4.0/emboss/server.ensemblgenomes EMBOSS-6.4.0/emboss/cacheensembl.c EMBOSS-6.4.0/ajax/ensembl/ensregistry.c EMBOSS-6.4.0/ajax/ensembl/ensregistry.c EMBOSS-6.4.0/ajax/ensembl/ensdatabaseadaptor.c EMBOSS-6.4.0/ajax/ensembl/ensdatabaseadaptor.h 10 Aug 2011: Microbial genomes use an enumerated species code which must be added to the query for data retrieval. This fix adds the species code to the comment field. In the next release a more complete solution will be implemented. Fix 8. EMBOSS-6.4.0/ajax/core/ajarch.h 10-Aug-2011: Corrects the size of long integers on Windows systems only. Fix 9. EMBOSS-6.4.0/emboss/cirdna.c 10-Aug-2011: Cirdna prints text inside solid blocks invisibly. When printed outside the text scaling was too small. The text scale is now adjusted for the radius and sequence length so that labels should be readable outside the box. Fix 10. EMBOSS-6.4.0/ajax/core/ajpat.c 10-Aug-2011: Fuzznuc, fuzzpro and fuzztran using a pattern file ignored the command line -mismatch qualifier for the first pattern. The default mismatch is now set to this value at the start of the pattern matching loop in the library. Fix 11. EMBOSS-6.4.0/ajax/core/ajfmt.c 11-Aug-2011: The function ajFmtScanF() handled va_list incorrectly. Only potentially affected code developers. From ajb at ebi.ac.uk Thu Aug 11 11:57:23 2011 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Thu, 11 Aug 2011 16:57:23 +0100 (BST) Subject: [EMBOSS] EMBOSS and mEMBOSS bug-fixes for 6.4.0 released Message-ID: <49000.82.26.12.214.1313078243.squirrel@imap04.ebi.ac.uk> UNIX users who downloaded the bug-fix patch file for EMBOSS earlier this afternoon may have found that there were compilation problems on a limited number of architectures. The patch has been amended slightly to hopefully fix this problem so please download it again if you were affected. If anyone continues to experience compilation problems then please let me know. Alan From alugena at aramayolab.org Fri Aug 19 19:38:33 2011 From: alugena at aramayolab.org (Aldrin Lugena) Date: Fri, 19 Aug 2011 18:38:33 -0500 Subject: [EMBOSS] a bug? Message-ID: Hi. Our lab installed the newest version of EMBOSS in our own server. When we type wossname, we get this: Finds programs by keywords in their short description Text to search for, or blank to list all programs: which is the right result. However, after typing "seqret" then hitting return, we are getting these: Error: /usr/local/bioinfosoft/emboss/share/EMBOSS/acd/seqrettype.acd: bad ACD relation '/edam/data/0000848 Sequence' Error: /usr/local/bioinfosoft/emboss/share/EMBOSS/acd/seqrettype.acd: bad ACD relation '/edam/data/0000849 Sequence record' Error: /usr/local/bioinfosoft/emboss/share/EMBOSS/acd/seqrettype.acd: bad ACD relation '/edam/data/0002178 1 or more' Error: /usr/local/bioinfosoft/emboss/share/EMBOSS/acd/sqltest.acd: bad ACD relation '/edam/topic/0000220 File handling' Error: /usr/local/bioinfosoft/emboss/share/EMBOSS/acd/sqltest.acd: bad ACD relation '/edam/operation/0000336 File debugging' Error: /usr/local/bioinfosoft/emboss/share/EMBOSS/acd/testplot.acd: bad ACD relation '/edam/topic/0000220 File handling' Error: /usr/local/bioinfosoft/emboss/share/EMBOSS/acd/testplot.acd: bad ACD relation '/edam/operation/0000336 File debugging' Error: /usr/local/bioinfosoft/emboss/share/EMBOSS/acd/testplot.acd: bad ACD relation '/edam/data/0002152 Rendering parameter' Error: /usr/local/bioinfosoft/emboss/share/EMBOSS/acd/testplot.acd: bad ACD relation '/edam/data/0002135 Toggle' Error: /usr/local/bioinfosoft/emboss/share/EMBOSS/acd/testplot.acd: bad ACD relation '/edam/data/0002142 EMBOSS graph' Error: /usr/local/bioinfosoft/emboss/share/EMBOSS/acd/treetypedisplay.acd: bad ACD relation '/edam/topic/0000220 File handling' Error: /usr/local/bioinfosoft/emboss/share/EMBOSS/acd/treetypedisplay.acd: bad ACD relation '/edam/operation/0000336 File debugging' Error: /usr/local/bioinfosoft/emboss/share/EMBOSS/acd/treetypedisplay.acd: bad ACD relation '/edam/data/0002142 EMBOSS graph' These are just a sample because there are tons of errors along the same lines. What is the reason for these errors? Also, what can we do to fix it? Thanks so much for reading this email. Hopefully to hear from someone soon. -Aldrin From pmr at ebi.ac.uk Sat Aug 20 15:39:20 2011 From: pmr at ebi.ac.uk (Peter Rice) Date: Sat, 20 Aug 2011 20:39:20 +0100 Subject: [EMBOSS] a bug? In-Reply-To: References: Message-ID: <4E500D68.3030004@ebi.ac.uk> On 20/08/2011 00:38, Aldrin Lugena wrote: > Hi. Our lab installed the newest version of EMBOSS in our own server. When > we type wossname, we get this: > > Finds programs by keywords in their short description > Text to search for, or blank to list all programs: > > which is the right result. > > However, after typing "seqret" then hitting return, we are getting these: > > Error: /usr/local/bioinfosoft/emboss/share/EMBOSS/acd/seqrettype.acd: bad > ACD relation '/edam/data/0000848 Sequence' All the files mentioned are from a previous release and should be deleted. The format of the ACD relations records changed in the new release. You can do that most easily by deleting all files in the /usr/local/bioinfosoft/emboss/share/EMBOSS/acd/ directory and then running "make install" from the emboss directory again to install all the ACD files for the new release. Do let us know (emboss-bug at emboss.open-bio.org) if that fails to fix it, or if you have any other problems or questions regards, Peter Rice EMBOSS Team From Alen.Zamanyan at loni.ucla.edu Mon Aug 29 19:49:53 2011 From: Alen.Zamanyan at loni.ucla.edu (Alen Zamanyan) Date: Mon, 29 Aug 2011 16:49:53 -0700 Subject: [EMBOSS] Standard Output Flag Message-ID: <39850C62545230468B1C5628660F7AC9028F5179B7C2@KAHLO.loni.ucla.edu> Hello, I am trying to run some EMBOSS tools on the command line (without a prompt). My goal is to have the tools print the output files to standard output. I noticed that the EMBOSS tools have the -stdout flag, but I can't seem to get anything printed to standard output. For instance, I tried the following commands, but to no avail: polydot globins.fasta -stdout Yes -auto Yes -graph cps tmap -stdout Yes -auto Yes opsd.msf -out tmap.res -graph cps chaos -auto Yes -stdout Yes tembl:j01636 -graph cps None of these executions write the results to standard out. Any ideas as to what I'm doing wrong? I appreciate, in advance, your time and assistance. Thanks, Alen From marko at cryst.bioc.cam.ac.uk Tue Aug 30 01:36:59 2011 From: marko at cryst.bioc.cam.ac.uk (Marko Hyvonen) Date: Tue, 30 Aug 2011 06:36:59 +0100 (BST) Subject: [EMBOSS] Standard Output Flag In-Reply-To: <39850C62545230468B1C5628660F7AC9028F5179B7C2@KAHLO.loni.ucla.edu> References: <39850C62545230468B1C5628660F7AC9028F5179B7C2@KAHLO.loni.ucla.edu> Message-ID: Dear Alen, I believe you should leave out the "Yes", although it might propt for outfile still, but offer stdout as default. You could also use (in Unix/Linux/etc at least) -outfile /dev/tty to direct the output to terminal. hth, Marko On Mon, 29 Aug 2011, Alen Zamanyan wrote: > Hello, > > I am trying to run some EMBOSS tools on the command line (without a prompt). My goal is to have the tools print the output files to standard output. I noticed that the EMBOSS tools have the -stdout flag, but I can't seem to get anything printed to standard output. For instance, I tried the following commands, but to no avail: > > polydot globins.fasta -stdout Yes -auto Yes -graph cps > tmap -stdout Yes -auto Yes opsd.msf -out tmap.res -graph cps > chaos -auto Yes -stdout Yes tembl:j01636 -graph cps > > None of these executions write the results to standard out. Any ideas as to what I'm doing wrong? I appreciate, in advance, your time and assistance. > > Thanks, > Alen > > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > _____________________________________ Marko Hyvonen Department of Biochemistry, University of Cambridge marko at cryst.bioc.cam.ac.uk http://www-cryst.bioc.cam.ac.uk/groups/hyvonen tel: +44-(0)1223-766 044 mobile: +44-(0)7796-174 877 fax: +44-(0)1223-766 002 -------------------------------------- From david.bauer at bayer.com Tue Aug 30 02:01:26 2011 From: david.bauer at bayer.com (david.bauer at bayer.com) Date: Tue, 30 Aug 2011 08:01:26 +0200 Subject: [EMBOSS] Antwort: Standard Output Flag In-Reply-To: <39850C62545230468B1C5628660F7AC9028F5179B7C2@KAHLO.loni.ucla.edu> Message-ID: Hello Alen, EMBOSS programs have 2 types of output: text (all programs) and graphics (some programs) You can direct the text output either to a file (-out tmap.res) or to standard output (-stdout) For graphical output you can choose the name of the graphics with -goutfile. The default graphics output is -graph x11 and goes to the X11 terminal. But as far as I know it is not possible to send the graphics to stdandard output. So if you want to post-process the postcript graphics the only choice is to send this to a file and then read from this file. Cheers, David. emboss-bounces at lists.open-bio.org schrieb am 30/08/2011 01:49:53: > Hello, > > I am trying to run some EMBOSS tools on the command line (without a > prompt). My goal is to have the tools print the output files to > standard output. I noticed that the EMBOSS tools have the -stdout > flag, but I can't seem to get anything printed to standard output. > For instance, I tried the following commands, but to no avail: > > polydot globins.fasta -stdout Yes -auto Yes -graph cps > tmap -stdout Yes -auto Yes opsd.msf -out tmap.res -graph cps > chaos -auto Yes -stdout Yes tembl:j01636 -graph cps > > None of these executions write the results to standard out. Any > ideas as to what I'm doing wrong? I appreciate, in advance, your > time and assistance. > > Thanks, > Alen > > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss From gbottu at vub.ac.be Tue Aug 30 14:00:18 2011 From: gbottu at vub.ac.be (Guy Bottu) Date: Tue, 30 Aug 2011 20:00:18 +0200 Subject: [EMBOSS] Antwort: Standard Output Flag In-Reply-To: References: Message-ID: <4E5D2532.5020505@vub.ac.be> david.bauer at bayer.com wrote: > The default graphics output is -graph x11 and goes to the X11 terminal. > But as far as I know it is not possible to send the graphics to stdandard > output. Well, it is actually possible : if you write -graph tekt you will get output for Tektronix terminals. If your terminal does not shift automatically from text mode to graphical mode you will get a lot of bizarre characters on your screen. This will of course not be useful :-) Cheers, Guy Bottu From ajb at ebi.ac.uk Thu Aug 11 13:20:31 2011 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Thu, 11 Aug 2011 14:20:31 +0100 (BST) Subject: [EMBOSS] EMBOSS and mEMBOSS bug-fixes for 6.4.0 released Message-ID: <53896.82.26.12.214.1313068831.squirrel@imap04.ebi.ac.uk> New bug-fix files are available for EMBOSS-6.4.0 and, for Windows users, a new version of mEMBOSS is available. The bugs fixed are appended for easy reference. 1) UNIX As usual, the most convenient way of applying the bug-fixes should be to apply the patch file: ftp://emboss.open-bio.org/pub/EMBOSS/fixes/patches/patch-1-11.gz to a freshly extracted copy of the EMBOSS-6.4.0.tar.gz source code and recompiling/installing. (see ftp://emboss.open-bio.org/pub/EMBOSS/fixes/patches/README.patch for instructions on using 'patch'). Alternatively, you can individually copy the patched files from the ftp://emboss.open-bio.org/pub/EMBOSS/fixes/ directory if your system does not support 'patch'. 2) mEMBOSS The new version incorporates all the bug-fixes listed below. Uninstall your previous mEMBOSS installation and download and install the new setup file from: ftp://emboss.open-bio.org/pub/EMBOSS/windows/mEMBOSS-6.4.0.2-setup.exe Alan ----------------------------------------------------------------------- Fix 1. EMBOSS-6.4.0/emboss/dbiflat.c EMBOSS-6.4.0/emboss/dbxflat.c 10 Aug 2011: The SwissProt description line format includes additional tags which interfere with the EMBL parser used in previous releases. The fix replaces this with a SwissProt parser that strips out the extra tags. After patching the release, any existing SwissProt description index files should be reindexed. Other indexes are unchanged. Fix 2. EMBOSS-6.4.0/ajax/core/ajquery.c 10 Aug 2011: For databases with more than one valid format (examples include the EBI dbfetch server) this fix allows the format to be specified with a qualifier on the command line. In the original release, only a format in the query string was used. Fix 3. EMBOSS-6.4.0/ajax/core/ajfeatread.c 10 Aug 2011: When parsing GFF3 format input, long feature tags (for example extremely long translations) exceeded limits in regular expression parsing. This fix decouples testing for escaped quotes from the main task of finding quoted strings. Fix 4. EMBOSS-6.4.0/emboss/data/Etcode.dat 10 Aug 2001: The local data file used by application tcode had a missing parameter line. Fix 5. EMBOSS-6.4.0/ajax/core/ajrange.c 10 Aug 2011: When sequence ranges (and possible highlighting for showalign) were in a list file, the parser overwrote string values. Fix 5. EMBOSS-6.4.0/ajax/core/ajseqabi.c 10 Aug 2011: Sample names in ABI format files were stored in incompletely defined strings. This fix corrects the string object. The sample name is also used as the sequence name. Fix 6. EMBOSS-6.4.0/emboss/dbxresource.c 10 Aug 2011: A future change to the format of Data Resource Catalogue entries in DRCAT.dat requires an update to the parsing of category lines. The current version is not affected. Fix 7. EMBOSS-6.4.0/emboss/server.ensemblgenomes EMBOSS-6.4.0/emboss/cacheensembl.c EMBOSS-6.4.0/ajax/ensembl/ensregistry.c EMBOSS-6.4.0/ajax/ensembl/ensregistry.c EMBOSS-6.4.0/ajax/ensembl/ensdatabaseadaptor.c EMBOSS-6.4.0/ajax/ensembl/ensdatabaseadaptor.h 10 Aug 2011: Microbial genomes use an enumerated species code which must be added to the query for data retrieval. This fix adds the species code to the comment field. In the next release a more complete solution will be implemented. Fix 8. EMBOSS-6.4.0/ajax/core/ajarch.h 10-Aug-2011: Corrects the size of long integers on Windows systems only. Fix 9. EMBOSS-6.4.0/emboss/cirdna.c 10-Aug-2011: Cirdna prints text inside solid blocks invisibly. When printed outside the text scaling was too small. The text scale is now adjusted for the radius and sequence length so that labels should be readable outside the box. Fix 10. EMBOSS-6.4.0/ajax/core/ajpat.c 10-Aug-2011: Fuzznuc, fuzzpro and fuzztran using a pattern file ignored the command line -mismatch qualifier for the first pattern. The default mismatch is now set to this value at the start of the pattern matching loop in the library. Fix 11. EMBOSS-6.4.0/ajax/core/ajfmt.c 11-Aug-2011: The function ajFmtScanF() handled va_list incorrectly. Only potentially affected code developers. From ajb at ebi.ac.uk Thu Aug 11 15:57:23 2011 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Thu, 11 Aug 2011 16:57:23 +0100 (BST) Subject: [EMBOSS] EMBOSS and mEMBOSS bug-fixes for 6.4.0 released Message-ID: <49000.82.26.12.214.1313078243.squirrel@imap04.ebi.ac.uk> UNIX users who downloaded the bug-fix patch file for EMBOSS earlier this afternoon may have found that there were compilation problems on a limited number of architectures. The patch has been amended slightly to hopefully fix this problem so please download it again if you were affected. If anyone continues to experience compilation problems then please let me know. Alan From alugena at aramayolab.org Fri Aug 19 23:38:33 2011 From: alugena at aramayolab.org (Aldrin Lugena) Date: Fri, 19 Aug 2011 18:38:33 -0500 Subject: [EMBOSS] a bug? Message-ID: Hi. Our lab installed the newest version of EMBOSS in our own server. When we type wossname, we get this: Finds programs by keywords in their short description Text to search for, or blank to list all programs: which is the right result. However, after typing "seqret" then hitting return, we are getting these: Error: /usr/local/bioinfosoft/emboss/share/EMBOSS/acd/seqrettype.acd: bad ACD relation '/edam/data/0000848 Sequence' Error: /usr/local/bioinfosoft/emboss/share/EMBOSS/acd/seqrettype.acd: bad ACD relation '/edam/data/0000849 Sequence record' Error: /usr/local/bioinfosoft/emboss/share/EMBOSS/acd/seqrettype.acd: bad ACD relation '/edam/data/0002178 1 or more' Error: /usr/local/bioinfosoft/emboss/share/EMBOSS/acd/sqltest.acd: bad ACD relation '/edam/topic/0000220 File handling' Error: /usr/local/bioinfosoft/emboss/share/EMBOSS/acd/sqltest.acd: bad ACD relation '/edam/operation/0000336 File debugging' Error: /usr/local/bioinfosoft/emboss/share/EMBOSS/acd/testplot.acd: bad ACD relation '/edam/topic/0000220 File handling' Error: /usr/local/bioinfosoft/emboss/share/EMBOSS/acd/testplot.acd: bad ACD relation '/edam/operation/0000336 File debugging' Error: /usr/local/bioinfosoft/emboss/share/EMBOSS/acd/testplot.acd: bad ACD relation '/edam/data/0002152 Rendering parameter' Error: /usr/local/bioinfosoft/emboss/share/EMBOSS/acd/testplot.acd: bad ACD relation '/edam/data/0002135 Toggle' Error: /usr/local/bioinfosoft/emboss/share/EMBOSS/acd/testplot.acd: bad ACD relation '/edam/data/0002142 EMBOSS graph' Error: /usr/local/bioinfosoft/emboss/share/EMBOSS/acd/treetypedisplay.acd: bad ACD relation '/edam/topic/0000220 File handling' Error: /usr/local/bioinfosoft/emboss/share/EMBOSS/acd/treetypedisplay.acd: bad ACD relation '/edam/operation/0000336 File debugging' Error: /usr/local/bioinfosoft/emboss/share/EMBOSS/acd/treetypedisplay.acd: bad ACD relation '/edam/data/0002142 EMBOSS graph' These are just a sample because there are tons of errors along the same lines. What is the reason for these errors? Also, what can we do to fix it? Thanks so much for reading this email. Hopefully to hear from someone soon. -Aldrin From pmr at ebi.ac.uk Sat Aug 20 19:39:20 2011 From: pmr at ebi.ac.uk (Peter Rice) Date: Sat, 20 Aug 2011 20:39:20 +0100 Subject: [EMBOSS] a bug? In-Reply-To: References: Message-ID: <4E500D68.3030004@ebi.ac.uk> On 20/08/2011 00:38, Aldrin Lugena wrote: > Hi. Our lab installed the newest version of EMBOSS in our own server. When > we type wossname, we get this: > > Finds programs by keywords in their short description > Text to search for, or blank to list all programs: > > which is the right result. > > However, after typing "seqret" then hitting return, we are getting these: > > Error: /usr/local/bioinfosoft/emboss/share/EMBOSS/acd/seqrettype.acd: bad > ACD relation '/edam/data/0000848 Sequence' All the files mentioned are from a previous release and should be deleted. The format of the ACD relations records changed in the new release. You can do that most easily by deleting all files in the /usr/local/bioinfosoft/emboss/share/EMBOSS/acd/ directory and then running "make install" from the emboss directory again to install all the ACD files for the new release. Do let us know (emboss-bug at emboss.open-bio.org) if that fails to fix it, or if you have any other problems or questions regards, Peter Rice EMBOSS Team From Alen.Zamanyan at loni.ucla.edu Mon Aug 29 23:49:53 2011 From: Alen.Zamanyan at loni.ucla.edu (Alen Zamanyan) Date: Mon, 29 Aug 2011 16:49:53 -0700 Subject: [EMBOSS] Standard Output Flag Message-ID: <39850C62545230468B1C5628660F7AC9028F5179B7C2@KAHLO.loni.ucla.edu> Hello, I am trying to run some EMBOSS tools on the command line (without a prompt). My goal is to have the tools print the output files to standard output. I noticed that the EMBOSS tools have the -stdout flag, but I can't seem to get anything printed to standard output. For instance, I tried the following commands, but to no avail: polydot globins.fasta -stdout Yes -auto Yes -graph cps tmap -stdout Yes -auto Yes opsd.msf -out tmap.res -graph cps chaos -auto Yes -stdout Yes tembl:j01636 -graph cps None of these executions write the results to standard out. Any ideas as to what I'm doing wrong? I appreciate, in advance, your time and assistance. Thanks, Alen From marko at cryst.bioc.cam.ac.uk Tue Aug 30 05:36:59 2011 From: marko at cryst.bioc.cam.ac.uk (Marko Hyvonen) Date: Tue, 30 Aug 2011 06:36:59 +0100 (BST) Subject: [EMBOSS] Standard Output Flag In-Reply-To: <39850C62545230468B1C5628660F7AC9028F5179B7C2@KAHLO.loni.ucla.edu> References: <39850C62545230468B1C5628660F7AC9028F5179B7C2@KAHLO.loni.ucla.edu> Message-ID: Dear Alen, I believe you should leave out the "Yes", although it might propt for outfile still, but offer stdout as default. You could also use (in Unix/Linux/etc at least) -outfile /dev/tty to direct the output to terminal. hth, Marko On Mon, 29 Aug 2011, Alen Zamanyan wrote: > Hello, > > I am trying to run some EMBOSS tools on the command line (without a prompt). My goal is to have the tools print the output files to standard output. I noticed that the EMBOSS tools have the -stdout flag, but I can't seem to get anything printed to standard output. For instance, I tried the following commands, but to no avail: > > polydot globins.fasta -stdout Yes -auto Yes -graph cps > tmap -stdout Yes -auto Yes opsd.msf -out tmap.res -graph cps > chaos -auto Yes -stdout Yes tembl:j01636 -graph cps > > None of these executions write the results to standard out. Any ideas as to what I'm doing wrong? I appreciate, in advance, your time and assistance. > > Thanks, > Alen > > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > _____________________________________ Marko Hyvonen Department of Biochemistry, University of Cambridge marko at cryst.bioc.cam.ac.uk http://www-cryst.bioc.cam.ac.uk/groups/hyvonen tel: +44-(0)1223-766 044 mobile: +44-(0)7796-174 877 fax: +44-(0)1223-766 002 -------------------------------------- From david.bauer at bayer.com Tue Aug 30 06:01:26 2011 From: david.bauer at bayer.com (david.bauer at bayer.com) Date: Tue, 30 Aug 2011 08:01:26 +0200 Subject: [EMBOSS] Antwort: Standard Output Flag In-Reply-To: <39850C62545230468B1C5628660F7AC9028F5179B7C2@KAHLO.loni.ucla.edu> Message-ID: Hello Alen, EMBOSS programs have 2 types of output: text (all programs) and graphics (some programs) You can direct the text output either to a file (-out tmap.res) or to standard output (-stdout) For graphical output you can choose the name of the graphics with -goutfile. The default graphics output is -graph x11 and goes to the X11 terminal. But as far as I know it is not possible to send the graphics to stdandard output. So if you want to post-process the postcript graphics the only choice is to send this to a file and then read from this file. Cheers, David. emboss-bounces at lists.open-bio.org schrieb am 30/08/2011 01:49:53: > Hello, > > I am trying to run some EMBOSS tools on the command line (without a > prompt). My goal is to have the tools print the output files to > standard output. I noticed that the EMBOSS tools have the -stdout > flag, but I can't seem to get anything printed to standard output. > For instance, I tried the following commands, but to no avail: > > polydot globins.fasta -stdout Yes -auto Yes -graph cps > tmap -stdout Yes -auto Yes opsd.msf -out tmap.res -graph cps > chaos -auto Yes -stdout Yes tembl:j01636 -graph cps > > None of these executions write the results to standard out. Any > ideas as to what I'm doing wrong? I appreciate, in advance, your > time and assistance. > > Thanks, > Alen > > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss From gbottu at vub.ac.be Tue Aug 30 18:00:18 2011 From: gbottu at vub.ac.be (Guy Bottu) Date: Tue, 30 Aug 2011 20:00:18 +0200 Subject: [EMBOSS] Antwort: Standard Output Flag In-Reply-To: References: Message-ID: <4E5D2532.5020505@vub.ac.be> david.bauer at bayer.com wrote: > The default graphics output is -graph x11 and goes to the X11 terminal. > But as far as I know it is not possible to send the graphics to stdandard > output. Well, it is actually possible : if you write -graph tekt you will get output for Tektronix terminals. If your terminal does not shift automatically from text mode to graphical mode you will get a lot of bizarre characters on your screen. This will of course not be useful :-) Cheers, Guy Bottu