From Lionel.Brooks at dartmouth.edu Wed Jan 5 13:46:08 2011 From: Lionel.Brooks at dartmouth.edu (Lionel (Lee) Brooks 3rd) Date: Wed, 05 Jan 2011 13:46:08 -0500 Subject: [EMBOSS] dbifasta error "too many parameters" Message-ID: <4D24BC70.2000901@dartmouth.edu> Hello Gentlepeople, I am interested in using regular expressions to search the human genome for occurrences of my favorite motif. I need coordinate values for each hit. I chose the EMBOSS program "dreg" for this task. I have a set of of fasta files; I have one fasta file per human chromosome. I wish to index these files with dbifasta so that I can use the dreg program for the regex search. I use the following command: me at mycpu$ dbifasta -dbname UCSC_hg19_softmask -idformat simple -directory /storage/EMBOSS/Emboss_DB -filenames *.fa -release hg19 -date 01/04/11 -outfile /storage/EMBOSS/Emboss_DB/logfile.dbifasta And receive the following error: Error: Argument 'seq01' : Too many parameters 2/1 ...the file that holds the chromosome sequences are named seq00.fa, seq01.fa, seq02.fa ... so on. Any sort of help is greatly appreciated. Thank you for your time in developing and maintaining this resource! -Lionel Brooks III Genetics Grad Student Dartmouth College From pmr at ebi.ac.uk Wed Jan 5 19:09:52 2011 From: pmr at ebi.ac.uk (Peter Rice) Date: Thu, 06 Jan 2011 00:09:52 +0000 Subject: [EMBOSS] dbifasta error "too many parameters" In-Reply-To: <4D24BC70.2000901@dartmouth.edu> References: <4D24BC70.2000901@dartmouth.edu> Message-ID: <4D250850.6060408@ebi.ac.uk> On 05/01/2011 18:46, Lionel (Lee) Brooks 3rd wrote: > I use the following command: > > me at mycpu$ dbifasta -dbname UCSC_hg19_softmask -idformat simple > -directory /storage/EMBOSS/Emboss_DB -filenames *.fa -release hg19 -date > 01/04/11 -outfile /storage/EMBOSS/Emboss_DB/logfile.dbifasta > > And receive the following error: > > Error: Argument 'seq01' : Too many parameters 2/1 > > ...the file that holds the chromosome sequences are named seq00.fa, > seq01.fa, seq02.fa ... so on. > Any sort of help is greatly appreciated. This is one of those Unix command line issues ... you need quotes around the "*.fa" (single or double quotes will do). The shell expands *.fa into the list of filenames before EMBOSS sees the results, and the second one is your "extra parameter". regards, Peter Rice EMBOSS team From wo.granon at gmail.com Wed Jan 12 12:16:14 2011 From: wo.granon at gmail.com (wo.granon at gmail.com) Date: Wed, 12 Jan 2011 18:16:14 +0100 Subject: [EMBOSS] error while loading shared libraries: libnucleus.so.6 Message-ID: Hello, I installed stable EMBOSS 6.3.1 on OpenSuse 11.3. ./configure, make and make install ran without an error. But when I try to run an EMBOSS app, i get the following error: # embossversion embossversion: error while loading shared libraries: libnucleus.so.6: cannot open shared object file: No such file or directory I think the attached output could help. Does anyone know what is wrong with my installation? Do you need additional data? Thanks, Wolfgang # ldd $(which embossversion) linux-gate.so.1 => (0xffffe000) libnucleus.so.6 => not found libacd.so.6 => not found libajaxdb.so.6 => not found libensembl.so.6 => not found libajaxg.so.6 => not found libajax.so.6 => not found libezlib.so.1 => not found libeexpat.so.1 => not found libepcre.so.7 => not found libeplplot.so.3 => not found libpq.so.5 => /usr/lib/libpq.so.5 (0xb77a4000) libX11.so.6 => /usr/lib/libX11.so.6 (0xb7669000) libgd.so.2 => /usr/lib/libgd.so.2 (0xb7622000) libpng14.so.14 => /usr/lib/libpng14.so.14 (0xb75f6000) libz.so.1 => /lib/libz.so.1 (0xb75e1000) libm.so.6 => /lib/libm.so.6 (0xb75b7000) libc.so.6 => /lib/libc.so.6 (0xb744c000) libssl.so.1.0.0 => /lib/libssl.so.1.0.0 (0xb73f5000) libcrypto.so.1.0.0 => /lib/libcrypto.so.1.0.0 (0xb7255000) libkrb5.so.3 => /usr/lib/libkrb5.so.3 (0xb718d000) libcom_err.so.2 => /lib/libcom_err.so.2 (0xb7187000) libgssapi_krb5.so.2 => /usr/lib/libgssapi_krb5.so.2 (0xb7150000) libldap_r-2.4.so.2 => /usr/lib/libldap_r-2.4.so.2 (0xb7100000) libpthread.so.0 => /lib/libpthread.so.0 (0xb70e5000) libxcb.so.1 => /usr/lib/libxcb.so.1 (0xb70c5000) libdl.so.2 => /lib/libdl.so.2 (0xb70bf000) libXpm.so.4 => /usr/lib/libXpm.so.4 (0xb70ac000) libjpeg.so.8 => /usr/lib/libjpeg.so.8 (0xb7073000) libfontconfig.so.1 => /usr/lib/libfontconfig.so.1 (0xb703d000) libfreetype.so.6 => /usr/lib/libfreetype.so.6 (0xb6fb6000) /lib/ld-linux.so.2 (0xb77e3000) libk5crypto.so.3 => /usr/lib/libk5crypto.so.3 (0xb6f8d000) libkrb5support.so.0 => /usr/lib/libkrb5support.so.0 (0xb6f84000) libkeyutils.so.1 => /lib/libkeyutils.so.1 (0xb6f80000) libresolv.so.2 => /lib/libresolv.so.2 (0xb6f69000) liblber-2.4.so.2 => /usr/lib/liblber-2.4.so.2 (0xb6f59000) libsasl2.so.2 => /usr/lib/libsasl2.so.2 (0xb6f3d000) libXau.so.6 => /usr/lib/libXau.so.6 (0xb6f39000) libexpat.so.1 => /lib/libexpat.so.1 (0xb6f0f000) From ajb at ebi.ac.uk Wed Jan 12 12:37:05 2011 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Wed, 12 Jan 2011 17:37:05 -0000 (UTC) Subject: [EMBOSS] error while loading shared libraries: libnucleus.so.6 In-Reply-To: References: Message-ID: <51851.86.26.12.63.1294853825.squirrel@webmail.ebi.ac.uk> Hello Wolfgang, On OpenSuse that error usually means you've installed EMBOSS into /usr/local such that the libraries are in /usr/local/lib. That library directory is cached on OpenSuse so all you should need to do is, with privilege, type "/sbin/ldconfig" to rebuild the cache. HTH Alan > Hello, > > I installed stable EMBOSS 6.3.1 on OpenSuse 11.3. > > ./configure, make and make install ran without an error. But when I > try to run an EMBOSS app, i get the following error: > > # embossversion > embossversion: error while loading shared libraries: libnucleus.so.6: > cannot open shared object file: No such file or directory > > I think the attached output could help. Does anyone know what is wrong > with my installation? Do you need additional data? > > Thanks, > Wolfgang > > # ldd $(which embossversion) > linux-gate.so.1 => (0xffffe000) > libnucleus.so.6 => not found > libacd.so.6 => not found > libajaxdb.so.6 => not found > libensembl.so.6 => not found > libajaxg.so.6 => not found > libajax.so.6 => not found > libezlib.so.1 => not found > libeexpat.so.1 => not found > libepcre.so.7 => not found > libeplplot.so.3 => not found > libpq.so.5 => /usr/lib/libpq.so.5 (0xb77a4000) > libX11.so.6 => /usr/lib/libX11.so.6 (0xb7669000) > libgd.so.2 => /usr/lib/libgd.so.2 (0xb7622000) > libpng14.so.14 => /usr/lib/libpng14.so.14 (0xb75f6000) > libz.so.1 => /lib/libz.so.1 (0xb75e1000) > libm.so.6 => /lib/libm.so.6 (0xb75b7000) > libc.so.6 => /lib/libc.so.6 (0xb744c000) > libssl.so.1.0.0 => /lib/libssl.so.1.0.0 (0xb73f5000) > libcrypto.so.1.0.0 => /lib/libcrypto.so.1.0.0 (0xb7255000) > libkrb5.so.3 => /usr/lib/libkrb5.so.3 (0xb718d000) > libcom_err.so.2 => /lib/libcom_err.so.2 (0xb7187000) > libgssapi_krb5.so.2 => /usr/lib/libgssapi_krb5.so.2 (0xb7150000) > libldap_r-2.4.so.2 => /usr/lib/libldap_r-2.4.so.2 (0xb7100000) > libpthread.so.0 => /lib/libpthread.so.0 (0xb70e5000) > libxcb.so.1 => /usr/lib/libxcb.so.1 (0xb70c5000) > libdl.so.2 => /lib/libdl.so.2 (0xb70bf000) > libXpm.so.4 => /usr/lib/libXpm.so.4 (0xb70ac000) > libjpeg.so.8 => /usr/lib/libjpeg.so.8 (0xb7073000) > libfontconfig.so.1 => /usr/lib/libfontconfig.so.1 (0xb703d000) > libfreetype.so.6 => /usr/lib/libfreetype.so.6 (0xb6fb6000) > /lib/ld-linux.so.2 (0xb77e3000) > libk5crypto.so.3 => /usr/lib/libk5crypto.so.3 (0xb6f8d000) > libkrb5support.so.0 => /usr/lib/libkrb5support.so.0 (0xb6f84000) > libkeyutils.so.1 => /lib/libkeyutils.so.1 (0xb6f80000) > libresolv.so.2 => /lib/libresolv.so.2 (0xb6f69000) > liblber-2.4.so.2 => /usr/lib/liblber-2.4.so.2 (0xb6f59000) > libsasl2.so.2 => /usr/lib/libsasl2.so.2 (0xb6f3d000) > libXau.so.6 => /usr/lib/libXau.so.6 (0xb6f39000) > libexpat.so.1 => /lib/libexpat.so.1 (0xb6f0f000) > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > From wo.granon at gmail.com Wed Jan 12 12:48:35 2011 From: wo.granon at gmail.com (wo.granon at gmail.com) Date: Wed, 12 Jan 2011 18:48:35 +0100 Subject: [EMBOSS] error while loading shared libraries: libnucleus.so.6 In-Reply-To: <51851.86.26.12.63.1294853825.squirrel@webmail.ebi.ac.uk> References: <51851.86.26.12.63.1294853825.squirrel@webmail.ebi.ac.uk> Message-ID: Thank you, that did the job! But now i have an other error for which i also can't find anything in the web: # embossversion Error: File /usr/share/EMBOSS/acd/embossversion.acd line 0: ACD file not opened Can you help me again? Thanks, Wolfgang 2011/1/12 : > Hello Wolfgang, > > On OpenSuse that error usually means you've installed EMBOSS into > /usr/local such that the libraries are in /usr/local/lib. That > library directory is cached on OpenSuse so all you should need to do is, > with privilege, type "/sbin/ldconfig" to rebuild the cache. > > HTH > > Alan > > > >> Hello, >> >> I installed stable EMBOSS 6.3.1 on OpenSuse 11.3. >> >> ./configure, make and make install ran without an error. But when I >> try to run an EMBOSS app, i get the following error: >> >> # embossversion >> embossversion: error while loading shared libraries: libnucleus.so.6: >> cannot open shared object file: No such file or directory >> >> I think the attached output could help. Does anyone know what is wrong >> with my installation? Do you need additional data? >> >> Thanks, >> Wolfgang >> >> # ldd $(which embossversion) >> ? ? ? ? linux-gate.so.1 => ?(0xffffe000) >> ? ? ? ? libnucleus.so.6 => not found >> ? ? ? ? libacd.so.6 => not found >> ? ? ? ? libajaxdb.so.6 => not found >> ? ? ? ? libensembl.so.6 => not found >> ? ? ? ? libajaxg.so.6 => not found >> ? ? ? ? libajax.so.6 => not found >> ? ? ? ? libezlib.so.1 => not found >> ? ? ? ? libeexpat.so.1 => not found >> ? ? ? ? libepcre.so.7 => not found >> ? ? ? ? libeplplot.so.3 => not found >> ? ? ? ? libpq.so.5 => /usr/lib/libpq.so.5 (0xb77a4000) >> ? ? ? ? libX11.so.6 => /usr/lib/libX11.so.6 (0xb7669000) >> ? ? ? ? libgd.so.2 => /usr/lib/libgd.so.2 (0xb7622000) >> ? ? ? ? libpng14.so.14 => /usr/lib/libpng14.so.14 (0xb75f6000) >> ? ? ? ? libz.so.1 => /lib/libz.so.1 (0xb75e1000) >> ? ? ? ? libm.so.6 => /lib/libm.so.6 (0xb75b7000) >> ? ? ? ? libc.so.6 => /lib/libc.so.6 (0xb744c000) >> ? ? ? ? libssl.so.1.0.0 => /lib/libssl.so.1.0.0 (0xb73f5000) >> ? ? ? ? libcrypto.so.1.0.0 => /lib/libcrypto.so.1.0.0 (0xb7255000) >> ? ? ? ? libkrb5.so.3 => /usr/lib/libkrb5.so.3 (0xb718d000) >> ? ? ? ? libcom_err.so.2 => /lib/libcom_err.so.2 (0xb7187000) >> ? ? ? ? libgssapi_krb5.so.2 => /usr/lib/libgssapi_krb5.so.2 (0xb7150000) >> ? ? ? ? libldap_r-2.4.so.2 => /usr/lib/libldap_r-2.4.so.2 (0xb7100000) >> ? ? ? ? libpthread.so.0 => /lib/libpthread.so.0 (0xb70e5000) >> ? ? ? ? libxcb.so.1 => /usr/lib/libxcb.so.1 (0xb70c5000) >> ? ? ? ? libdl.so.2 => /lib/libdl.so.2 (0xb70bf000) >> ? ? ? ? libXpm.so.4 => /usr/lib/libXpm.so.4 (0xb70ac000) >> ? ? ? ? libjpeg.so.8 => /usr/lib/libjpeg.so.8 (0xb7073000) >> ? ? ? ? libfontconfig.so.1 => /usr/lib/libfontconfig.so.1 (0xb703d000) >> ? ? ? ? libfreetype.so.6 => /usr/lib/libfreetype.so.6 (0xb6fb6000) >> ? ? ? ? /lib/ld-linux.so.2 (0xb77e3000) >> ? ? ? ? libk5crypto.so.3 => /usr/lib/libk5crypto.so.3 (0xb6f8d000) >> ? ? ? ? libkrb5support.so.0 => /usr/lib/libkrb5support.so.0 (0xb6f84000) >> ? ? ? ? libkeyutils.so.1 => /lib/libkeyutils.so.1 (0xb6f80000) >> ? ? ? ? libresolv.so.2 => /lib/libresolv.so.2 (0xb6f69000) >> ? ? ? ? liblber-2.4.so.2 => /usr/lib/liblber-2.4.so.2 (0xb6f59000) >> ? ? ? ? libsasl2.so.2 => /usr/lib/libsasl2.so.2 (0xb6f3d000) >> ? ? ? ? libXau.so.6 => /usr/lib/libXau.so.6 (0xb6f39000) >> ? ? ? ? libexpat.so.1 => /lib/libexpat.so.1 (0xb6f0f000) >> _______________________________________________ >> EMBOSS mailing list >> EMBOSS at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/emboss >> > > > From wo.granon at gmail.com Wed Jan 12 13:28:42 2011 From: wo.granon at gmail.com (wo.granon at gmail.com) Date: Wed, 12 Jan 2011 19:28:42 +0100 Subject: [EMBOSS] error while loading shared libraries: libnucleus.so.6 In-Reply-To: <45813.86.26.12.63.1294856077.squirrel@webmail.ebi.ac.uk> References: <51851.86.26.12.63.1294853825.squirrel@webmail.ebi.ac.uk> <45813.86.26.12.63.1294856077.squirrel@webmail.ebi.ac.uk> Message-ID: Thank you for your help. Really strange. Following situation: # ls /usr/share/EMBOSS/ emboss.default # ls /usr/local/share/EMBOSS/ acd data doc emboss.default.template jemboss plstnd5.fnt plxtnd5.fnt test Then i looked into /usr/share/EMBOSS/emboss.default, but there is no variable EMBOSS_ACDROOT set. Could it be set elsewhere? Thanks, Wolfgang 2011/1/12 : > Well if you've installed to /usr/local then it should be > looking for that file in /usr/local/share/EMBOSS/acd/embossversion.acd > > As it's looking under /usr/share... my first suspicion would be that > you've set an environment variable incorrectly (e.g. > EMBOSS_ACDROOT). You should not really need to set any EMBOSS > environment variables, it should work OK without. So, if > you have set any such envvars then try unsetting them and run > the program again. > > Alan > > > > >> Thank you, that did the job! But now i have an other error for which i >> also can't find anything in the web: >> >> # embossversion >> Error: File /usr/share/EMBOSS/acd/embossversion.acd line 0: ACD file not >> opened >> >> Can you help me again? >> >> Thanks, >> Wolfgang >> >> 2011/1/12 ?: >>> Hello Wolfgang, >>> >>> On OpenSuse that error usually means you've installed EMBOSS into >>> /usr/local such that the libraries are in /usr/local/lib. That >>> library directory is cached on OpenSuse so all you should need to do is, >>> with privilege, type "/sbin/ldconfig" to rebuild the cache. >>> >>> HTH >>> >>> Alan >>> >>> >>> >>>> Hello, >>>> >>>> I installed stable EMBOSS 6.3.1 on OpenSuse 11.3. >>>> >>>> ./configure, make and make install ran without an error. But when I >>>> try to run an EMBOSS app, i get the following error: >>>> >>>> # embossversion >>>> embossversion: error while loading shared libraries: libnucleus.so.6: >>>> cannot open shared object file: No such file or directory >>>> >>>> I think the attached output could help. Does anyone know what is wrong >>>> with my installation? Do you need additional data? >>>> >>>> Thanks, >>>> Wolfgang >>>> >>>> # ldd $(which embossversion) >>>> ? ? ? ? linux-gate.so.1 => ?(0xffffe000) >>>> ? ? ? ? libnucleus.so.6 => not found >>>> ? ? ? ? libacd.so.6 => not found >>>> ? ? ? ? libajaxdb.so.6 => not found >>>> ? ? ? ? libensembl.so.6 => not found >>>> ? ? ? ? libajaxg.so.6 => not found >>>> ? ? ? ? libajax.so.6 => not found >>>> ? ? ? ? libezlib.so.1 => not found >>>> ? ? ? ? libeexpat.so.1 => not found >>>> ? ? ? ? libepcre.so.7 => not found >>>> ? ? ? ? libeplplot.so.3 => not found >>>> ? ? ? ? libpq.so.5 => /usr/lib/libpq.so.5 (0xb77a4000) >>>> ? ? ? ? libX11.so.6 => /usr/lib/libX11.so.6 (0xb7669000) >>>> ? ? ? ? libgd.so.2 => /usr/lib/libgd.so.2 (0xb7622000) >>>> ? ? ? ? libpng14.so.14 => /usr/lib/libpng14.so.14 (0xb75f6000) >>>> ? ? ? ? libz.so.1 => /lib/libz.so.1 (0xb75e1000) >>>> ? ? ? ? libm.so.6 => /lib/libm.so.6 (0xb75b7000) >>>> ? ? ? ? libc.so.6 => /lib/libc.so.6 (0xb744c000) >>>> ? ? ? ? libssl.so.1.0.0 => /lib/libssl.so.1.0.0 (0xb73f5000) >>>> ? ? ? ? libcrypto.so.1.0.0 => /lib/libcrypto.so.1.0.0 (0xb7255000) >>>> ? ? ? ? libkrb5.so.3 => /usr/lib/libkrb5.so.3 (0xb718d000) >>>> ? ? ? ? libcom_err.so.2 => /lib/libcom_err.so.2 (0xb7187000) >>>> ? ? ? ? libgssapi_krb5.so.2 => /usr/lib/libgssapi_krb5.so.2 >>>> (0xb7150000) >>>> ? ? ? ? libldap_r-2.4.so.2 => /usr/lib/libldap_r-2.4.so.2 (0xb7100000) >>>> ? ? ? ? libpthread.so.0 => /lib/libpthread.so.0 (0xb70e5000) >>>> ? ? ? ? libxcb.so.1 => /usr/lib/libxcb.so.1 (0xb70c5000) >>>> ? ? ? ? libdl.so.2 => /lib/libdl.so.2 (0xb70bf000) >>>> ? ? ? ? libXpm.so.4 => /usr/lib/libXpm.so.4 (0xb70ac000) >>>> ? ? ? ? libjpeg.so.8 => /usr/lib/libjpeg.so.8 (0xb7073000) >>>> ? ? ? ? libfontconfig.so.1 => /usr/lib/libfontconfig.so.1 (0xb703d000) >>>> ? ? ? ? libfreetype.so.6 => /usr/lib/libfreetype.so.6 (0xb6fb6000) >>>> ? ? ? ? /lib/ld-linux.so.2 (0xb77e3000) >>>> ? ? ? ? libk5crypto.so.3 => /usr/lib/libk5crypto.so.3 (0xb6f8d000) >>>> ? ? ? ? libkrb5support.so.0 => /usr/lib/libkrb5support.so.0 >>>> (0xb6f84000) >>>> ? ? ? ? libkeyutils.so.1 => /lib/libkeyutils.so.1 (0xb6f80000) >>>> ? ? ? ? libresolv.so.2 => /lib/libresolv.so.2 (0xb6f69000) >>>> ? ? ? ? liblber-2.4.so.2 => /usr/lib/liblber-2.4.so.2 (0xb6f59000) >>>> ? ? ? ? libsasl2.so.2 => /usr/lib/libsasl2.so.2 (0xb6f3d000) >>>> ? ? ? ? libXau.so.6 => /usr/lib/libXau.so.6 (0xb6f39000) >>>> ? ? ? ? libexpat.so.1 => /lib/libexpat.so.1 (0xb6f0f000) >>>> _______________________________________________ >>>> EMBOSS mailing list >>>> EMBOSS at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/emboss >>>> >>> >>> >>> >> > > > From wo.granon at gmail.com Wed Jan 12 13:41:47 2011 From: wo.granon at gmail.com (wo.granon at gmail.com) Date: Wed, 12 Jan 2011 19:41:47 +0100 Subject: [EMBOSS] error while loading shared libraries: libnucleus.so.6 In-Reply-To: References: <51851.86.26.12.63.1294853825.squirrel@webmail.ebi.ac.uk> <45813.86.26.12.63.1294856077.squirrel@webmail.ebi.ac.uk> Message-ID: Thank you, problem solved. Starting the system new solved the problem ;-) There must have been some variables from a previous installation set. Wolfgang 2011/1/12 : > Thank you for your help. Really strange. > > Following situation: > # ls ?/usr/share/EMBOSS/ > emboss.default > # ls /usr/local/share/EMBOSS/ > acd ?data ?doc ?emboss.default.template ?jemboss ?plstnd5.fnt ?plxtnd5.fnt ?test > > Then i looked into /usr/share/EMBOSS/emboss.default, but there is no > variable EMBOSS_ACDROOT set. Could it be set elsewhere? > > Thanks, > Wolfgang > > > > > > 2011/1/12 ?: >> Well if you've installed to /usr/local then it should be >> looking for that file in /usr/local/share/EMBOSS/acd/embossversion.acd >> >> As it's looking under /usr/share... my first suspicion would be that >> you've set an environment variable incorrectly (e.g. >> EMBOSS_ACDROOT). You should not really need to set any EMBOSS >> environment variables, it should work OK without. So, if >> you have set any such envvars then try unsetting them and run >> the program again. >> >> Alan >> >> >> >> >>> Thank you, that did the job! But now i have an other error for which i >>> also can't find anything in the web: >>> >>> # embossversion >>> Error: File /usr/share/EMBOSS/acd/embossversion.acd line 0: ACD file not >>> opened >>> >>> Can you help me again? >>> >>> Thanks, >>> Wolfgang >>> >>> 2011/1/12 ?: >>>> Hello Wolfgang, >>>> >>>> On OpenSuse that error usually means you've installed EMBOSS into >>>> /usr/local such that the libraries are in /usr/local/lib. That >>>> library directory is cached on OpenSuse so all you should need to do is, >>>> with privilege, type "/sbin/ldconfig" to rebuild the cache. >>>> >>>> HTH >>>> >>>> Alan >>>> >>>> >>>> >>>>> Hello, >>>>> >>>>> I installed stable EMBOSS 6.3.1 on OpenSuse 11.3. >>>>> >>>>> ./configure, make and make install ran without an error. But when I >>>>> try to run an EMBOSS app, i get the following error: >>>>> >>>>> # embossversion >>>>> embossversion: error while loading shared libraries: libnucleus.so.6: >>>>> cannot open shared object file: No such file or directory >>>>> >>>>> I think the attached output could help. Does anyone know what is wrong >>>>> with my installation? Do you need additional data? >>>>> >>>>> Thanks, >>>>> Wolfgang >>>>> >>>>> # ldd $(which embossversion) >>>>> ? ? ? ? linux-gate.so.1 => ?(0xffffe000) >>>>> ? ? ? ? libnucleus.so.6 => not found >>>>> ? ? ? ? libacd.so.6 => not found >>>>> ? ? ? ? libajaxdb.so.6 => not found >>>>> ? ? ? ? libensembl.so.6 => not found >>>>> ? ? ? ? libajaxg.so.6 => not found >>>>> ? ? ? ? libajax.so.6 => not found >>>>> ? ? ? ? libezlib.so.1 => not found >>>>> ? ? ? ? libeexpat.so.1 => not found >>>>> ? ? ? ? libepcre.so.7 => not found >>>>> ? ? ? ? libeplplot.so.3 => not found >>>>> ? ? ? ? libpq.so.5 => /usr/lib/libpq.so.5 (0xb77a4000) >>>>> ? ? ? ? libX11.so.6 => /usr/lib/libX11.so.6 (0xb7669000) >>>>> ? ? ? ? libgd.so.2 => /usr/lib/libgd.so.2 (0xb7622000) >>>>> ? ? ? ? libpng14.so.14 => /usr/lib/libpng14.so.14 (0xb75f6000) >>>>> ? ? ? ? libz.so.1 => /lib/libz.so.1 (0xb75e1000) >>>>> ? ? ? ? libm.so.6 => /lib/libm.so.6 (0xb75b7000) >>>>> ? ? ? ? libc.so.6 => /lib/libc.so.6 (0xb744c000) >>>>> ? ? ? ? libssl.so.1.0.0 => /lib/libssl.so.1.0.0 (0xb73f5000) >>>>> ? ? ? ? libcrypto.so.1.0.0 => /lib/libcrypto.so.1.0.0 (0xb7255000) >>>>> ? ? ? ? libkrb5.so.3 => /usr/lib/libkrb5.so.3 (0xb718d000) >>>>> ? ? ? ? libcom_err.so.2 => /lib/libcom_err.so.2 (0xb7187000) >>>>> ? ? ? ? libgssapi_krb5.so.2 => /usr/lib/libgssapi_krb5.so.2 >>>>> (0xb7150000) >>>>> ? ? ? ? libldap_r-2.4.so.2 => /usr/lib/libldap_r-2.4.so.2 (0xb7100000) >>>>> ? ? ? ? libpthread.so.0 => /lib/libpthread.so.0 (0xb70e5000) >>>>> ? ? ? ? libxcb.so.1 => /usr/lib/libxcb.so.1 (0xb70c5000) >>>>> ? ? ? ? libdl.so.2 => /lib/libdl.so.2 (0xb70bf000) >>>>> ? ? ? ? libXpm.so.4 => /usr/lib/libXpm.so.4 (0xb70ac000) >>>>> ? ? ? ? libjpeg.so.8 => /usr/lib/libjpeg.so.8 (0xb7073000) >>>>> ? ? ? ? libfontconfig.so.1 => /usr/lib/libfontconfig.so.1 (0xb703d000) >>>>> ? ? ? ? libfreetype.so.6 => /usr/lib/libfreetype.so.6 (0xb6fb6000) >>>>> ? ? ? ? /lib/ld-linux.so.2 (0xb77e3000) >>>>> ? ? ? ? libk5crypto.so.3 => /usr/lib/libk5crypto.so.3 (0xb6f8d000) >>>>> ? ? ? ? libkrb5support.so.0 => /usr/lib/libkrb5support.so.0 >>>>> (0xb6f84000) >>>>> ? ? ? ? libkeyutils.so.1 => /lib/libkeyutils.so.1 (0xb6f80000) >>>>> ? ? ? ? libresolv.so.2 => /lib/libresolv.so.2 (0xb6f69000) >>>>> ? ? ? ? liblber-2.4.so.2 => /usr/lib/liblber-2.4.so.2 (0xb6f59000) >>>>> ? ? ? ? libsasl2.so.2 => /usr/lib/libsasl2.so.2 (0xb6f3d000) >>>>> ? ? ? ? libXau.so.6 => /usr/lib/libXau.so.6 (0xb6f39000) >>>>> ? ? ? ? libexpat.so.1 => /lib/libexpat.so.1 (0xb6f0f000) >>>>> _______________________________________________ >>>>> EMBOSS mailing list >>>>> EMBOSS at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/emboss >>>>> >>>> >>>> >>>> >>> >> >> >> > From wo.granon at gmail.com Sun Jan 16 06:45:57 2011 From: wo.granon at gmail.com (wo.granon at gmail.com) Date: Sun, 16 Jan 2011 12:45:57 +0100 Subject: [EMBOSS] cirdna and Text inside or outside of blocks In-Reply-To: References: Message-ID: Hello, I have following problem with cirdna an Text inside or outside of blocks: If I use the example input file from the manual: http://emboss.sourceforge.net/apps/release/6.3/emboss/apps/cirdna.html#input.1 and "-posblocks 1" the given block text ist _not_ printed. If I use "-posblocks 2" the text is printed, but in a not readable way: http://tinypic.com/r/20t5wzs/7 Can you tell me what I do wrong or if this is a bug? Thanks, Wolfgang From wo.granon at gmail.com Sun Jan 16 07:56:07 2011 From: wo.granon at gmail.com (wo.granon at gmail.com) Date: Sun, 16 Jan 2011 13:56:07 +0100 Subject: [EMBOSS] cirdna and Text inside or outside of blocks In-Reply-To: References: Message-ID: Here a little bigger: http://tinypic.com/r/2010x8n/7 It looks like that there is no space between the characters. Thanks, Wolfgang 2011/1/16 : > Hello, > > I have following problem with cirdna an Text inside or outside of blocks: > > If I use the example input file from the manual: > http://emboss.sourceforge.net/apps/release/6.3/emboss/apps/cirdna.html#input.1 > > and "-posblocks 1" the given block text ist _not_ printed. If I use > "-posblocks 2" the text is printed, but in a not readable way: > http://tinypic.com/r/20t5wzs/7 > > Can you tell me what I do wrong or if this is a bug? > > Thanks, > Wolfgang > From stephen.taylor at imm.ox.ac.uk Wed Jan 19 11:09:01 2011 From: stephen.taylor at imm.ox.ac.uk (Stephen Taylor) Date: Wed, 19 Jan 2011 16:09:01 +0000 Subject: [EMBOSS] SAM format Message-ID: <4D370C9D.5080902@imm.ox.ac.uk> Hi, Is EMBOSS planning to release tools that produce SAM format in the near future or is it more likely to be on the customary July 15th release? Kind regards and thanks, Steve From pmr at ebi.ac.uk Thu Jan 20 03:16:39 2011 From: pmr at ebi.ac.uk (Peter Rice) Date: Thu, 20 Jan 2011 08:16:39 +0000 Subject: [EMBOSS] SAM format In-Reply-To: <4D370C9D.5080902@imm.ox.ac.uk> References: <4D370C9D.5080902@imm.ox.ac.uk> Message-ID: <4D37EF67.1080206@ebi.ac.uk> On 01/19/11 16:09, Stephen Taylor wrote: > Hi, > > Is EMBOSS planning to release tools that produce SAM format in the near > future or is it more likely to be on the customary July 15th release? The last release EMBOSS 6.3.1 has SAM as an output format for sequences and pairwise alignments (-oformat sam and -aformat sam respectively). What data would you like to represent in SAM format, and are there extra fields you would like us to include? regards, Peter Rice From stephen.taylor at imm.ox.ac.uk Thu Jan 20 04:06:59 2011 From: stephen.taylor at imm.ox.ac.uk (Stephen Taylor) Date: Thu, 20 Jan 2011 09:06:59 +0000 Subject: [EMBOSS] SAM format In-Reply-To: <4D37EF67.1080206@ebi.ac.uk> References: <4D370C9D.5080902@imm.ox.ac.uk> <4D37EF67.1080206@ebi.ac.uk> Message-ID: <4D37FB33.8060801@imm.ox.ac.uk> Hi Peter, >> >> Is EMBOSS planning to release tools that produce SAM format in the near >> future or is it more likely to be on the customary July 15th release? > > The last release EMBOSS 6.3.1 has SAM as an output format for sequences > and pairwise alignments (-oformat sam and -aformat sam respectively). > > What data would you like to represent in SAM format, and are there extra > fields you would like us to include? > So it does! Excellent. Sadly, fuzznuc doesn't seem to work using aformat or oformat. Is that due to be supported? Thanks, Steve From pmr at ebi.ac.uk Thu Jan 20 04:36:00 2011 From: pmr at ebi.ac.uk (Peter Rice) Date: Thu, 20 Jan 2011 09:36:00 +0000 Subject: [EMBOSS] SAM format In-Reply-To: <4D37FB33.8060801@imm.ox.ac.uk> References: <4D370C9D.5080902@imm.ox.ac.uk> <4D37EF67.1080206@ebi.ac.uk> <4D37FB33.8060801@imm.ox.ac.uk> Message-ID: <4D380200.7080806@ebi.ac.uk> On 01/20/11 09:06, Stephen Taylor wrote: > Hi Peter, > >>> >>> Is EMBOSS planning to release tools that produce SAM format in the near >>> future or is it more likely to be on the customary July 15th release? >> >> The last release EMBOSS 6.3.1 has SAM as an output format for sequences >> and pairwise alignments (-oformat sam and -aformat sam respectively). ... oops, -osformat for sequences of course. > Sadly, fuzznuc doesn't seem to work using aformat or oformat. Is that > due to be supported? Ah, fuzznuc reports features so we hadn't implemented SAM there. However, you can use -rformat listfile to get USAs for the features, and then seqret -osformat sam @listfilename to get the sequences in SAM format. Possibly scope to do more there. What would you like to see in SAM output for fuzznuc? regards, Peter From pmr at ebi.ac.uk Thu Jan 20 04:40:35 2011 From: pmr at ebi.ac.uk (Peter Rice) Date: Thu, 20 Jan 2011 09:40:35 +0000 Subject: [EMBOSS] SAM format In-Reply-To: <4D37FDB9.7000804@imm.ox.ac.uk> References: <4D370C9D.5080902@imm.ox.ac.uk> <4D37EF67.1080206@ebi.ac.uk> <4D37FDB9.7000804@imm.ox.ac.uk> Message-ID: <4D380313.7030106@ebi.ac.uk> On 01/20/11 09:17, Stephen Taylor wrote: > Is there a bug in the gff3 output of fuzznuc? > > ##gff-version 3 > ##sequence-region chr21 1 46944323 > #!Date 2011-01-20 > #!Type DNA > #!Source-version EMBOSS 6.3.1 > chr21 fuzznuc nucleotide_motif 13362906 13362942 37.000 + . ID="chr21.1";note="*pat pattern" > > It would be nice to actually show the pattern matched in the note field. or both. What it shows is the "name" of the pattern, which usually defaults to pattern. We could show the name and then the pattern. I will add it to the next release. Thanks for the suggestion. Peter From stephen.taylor at imm.ox.ac.uk Thu Jan 20 04:17:45 2011 From: stephen.taylor at imm.ox.ac.uk (Stephen Taylor) Date: Thu, 20 Jan 2011 09:17:45 +0000 Subject: [EMBOSS] SAM format In-Reply-To: <4D37EF67.1080206@ebi.ac.uk> References: <4D370C9D.5080902@imm.ox.ac.uk> <4D37EF67.1080206@ebi.ac.uk> Message-ID: <4D37FDB9.7000804@imm.ox.ac.uk> On 20/01/2011 08:16, Peter Rice wrote: > On 01/19/11 16:09, Stephen Taylor wrote: >> Hi, >> >> Is EMBOSS planning to release tools that produce SAM format in the near >> future or is it more likely to be on the customary July 15th release? > > The last release EMBOSS 6.3.1 has SAM as an output format for sequences > and pairwise alignments (-oformat sam and -aformat sam respectively). > > What data would you like to represent in SAM format, and are there extra > fields you would like us to include? Also... Is there a bug in the gff3 output of fuzznuc? ##gff-version 3 ##sequence-region chr21 1 46944323 #!Date 2011-01-20 #!Type DNA #!Source-version EMBOSS 6.3.1 chr21 fuzznuc nucleotide_motif 13362906 13362942 37.000 + . ID="chr21.1";note="*pat pattern" It would be nice to actually show the pattern matched in the note field. Thanks, Steve From stephen.taylor at imm.ox.ac.uk Thu Jan 20 05:36:20 2011 From: stephen.taylor at imm.ox.ac.uk (Stephen Taylor) Date: Thu, 20 Jan 2011 10:36:20 +0000 Subject: [EMBOSS] SAM format In-Reply-To: <4D380200.7080806@ebi.ac.uk> References: <4D370C9D.5080902@imm.ox.ac.uk> <4D37EF67.1080206@ebi.ac.uk> <4D37FB33.8060801@imm.ox.ac.uk> <4D380200.7080806@ebi.ac.uk> Message-ID: <4D381024.1010001@imm.ox.ac.uk> On 20/01/2011 09:36, Peter Rice wrote: > On 01/20/11 09:06, Stephen Taylor wrote: >> Hi Peter, >> >>>> >>>> Is EMBOSS planning to release tools that produce SAM format in the near >>>> future or is it more likely to be on the customary July 15th release? >>> >>> The last release EMBOSS 6.3.1 has SAM as an output format for sequences >>> and pairwise alignments (-oformat sam and -aformat sam respectively). > > ... oops, -osformat for sequences of course. > > >> Sadly, fuzznuc doesn't seem to work using aformat or oformat. Is that >> due to be supported? > > Ah, fuzznuc reports features so we hadn't implemented SAM there. > > However, you can use -rformat listfile to get USAs for the features, and > then seqret -osformat sam @listfilename to get the sequences in SAM format. > > Possibly scope to do more there. What would you like to see in SAM > output for fuzznuc? My motivation was to build BAM tracks showing matches of lots of patterns in the genome sequence. I hadn't thought about proteins but I guess you could so something similar. The SAM file would show the position of each match per line and the CIGAR string containing the matched pattern and SEQ (col 10) containing the query pattern expanded to show the match. The original pattern could be in the OPT field. I see there is a tag for Mismatching positions (MD) which would work for regex style matches (so good for 'dreg'), but I am not sure it would be strictly legal for a PROSITE like pattern. e.g for [CG](5)TG{A}N(1,5)C Could you have MD:Z:[CG](5)TG{A}N(1,5)C ? It looks like {,} is not allowed. So perhaps you would have to translate the pattern to a regex or generate an alternative optional tag. I am not a SAM expert so apologies if I am proposing to violate the format rules! Incidentally, I would use dreg but it doesn't allow mismatches to be easily specified. Steve From pmr at ebi.ac.uk Thu Jan 20 05:54:33 2011 From: pmr at ebi.ac.uk (Peter Rice) Date: Thu, 20 Jan 2011 10:54:33 +0000 Subject: [EMBOSS] SAM format In-Reply-To: <4D381024.1010001@imm.ox.ac.uk> References: <4D370C9D.5080902@imm.ox.ac.uk> <4D37EF67.1080206@ebi.ac.uk> <4D37FB33.8060801@imm.ox.ac.uk> <4D380200.7080806@ebi.ac.uk> <4D381024.1010001@imm.ox.ac.uk> Message-ID: <4D381469.2020503@ebi.ac.uk> On 01/20/11 10:36, Stephen Taylor wrote: > On 20/01/2011 09:36, Peter Rice wrote: >> Possibly scope to do more there. What would you like to see in SAM >> output for fuzznuc? > > My motivation was to build BAM tracks showing matches of lots of > patterns in the genome sequence. I hadn't thought about proteins but I > guess you could so something similar. > > The SAM file would show the position of each match per line and the > CIGAR string containing the matched pattern and SEQ (col 10) containing > the query pattern expanded to show the match. The original pattern could > be in the OPT field. Interesting. The sequence becomes the reference. We would have to do a little extra work to generate the CIGAR string for various patterns but that should be possible but modifying the pattern matching code. >I see there is a tag for Mismatching positions (MD) > which would work for regex style matches (so good for 'dreg'), but I am > not sure it would be strictly legal for a PROSITE like pattern. > > e.g for [CG](5)TG{A}N(1,5)C > > Could you have > > MD:Z:[CG](5)TG{A}N(1,5)C That will need some investigation. Maybe prosite patterns can be translated to regex for this purpose - many will convert easily. > It looks like {,} is not allowed. So perhaps you would have to translate > the pattern to a regex or generate an alternative optional tag. I am not > a SAM expert so apologies if I am proposing to violate the format rules! N(1,5) is equivalent to NN?N?N?N? ... though prosite ranges can go over 100 positions. > Incidentally, I would use dreg but it doesn't allow mismatches to be > easily specified. True, that's a regular expression library issue. regards, Peter From stephen.taylor at imm.ox.ac.uk Mon Jan 24 06:09:05 2011 From: stephen.taylor at imm.ox.ac.uk (Stephen Taylor) Date: Mon, 24 Jan 2011 11:09:05 +0000 Subject: [EMBOSS] SAM format In-Reply-To: <4D380313.7030106@ebi.ac.uk> References: <4D370C9D.5080902@imm.ox.ac.uk> <4D37EF67.1080206@ebi.ac.uk> <4D37FDB9.7000804@imm.ox.ac.uk> <4D380313.7030106@ebi.ac.uk> Message-ID: <4D3D5DD1.8090303@imm.ox.ac.uk> Hi again Peter, > On 01/20/11 09:17, Stephen Taylor wrote: > >> Is there a bug in the gff3 output of fuzznuc? >> >> ##gff-version 3 >> ##sequence-region chr21 1 46944323 >> #!Date 2011-01-20 >> #!Type DNA >> #!Source-version EMBOSS 6.3.1 >> chr21 fuzznuc nucleotide_motif 13362906 13362942 37.000 + . ID="chr21.1";note="*pat pattern" >> >> It would be nice to actually show the pattern matched in the note field. > > or both. What it shows is the "name" of the pattern, which usually > defaults to pattern. Please can you define 'usually' i.e. What are the 'rules' for getting it to show the pattern? Usual behaviour when I run it, is it shows note="*pat pattern". Thanks, Steve From pmr at ebi.ac.uk Mon Jan 24 06:45:39 2011 From: pmr at ebi.ac.uk (Peter Rice) Date: Mon, 24 Jan 2011 11:45:39 +0000 Subject: [EMBOSS] SAM format In-Reply-To: <4D3D5DD1.8090303@imm.ox.ac.uk> References: <4D370C9D.5080902@imm.ox.ac.uk> <4D37EF67.1080206@ebi.ac.uk> <4D37FDB9.7000804@imm.ox.ac.uk> <4D380313.7030106@ebi.ac.uk> <4D3D5DD1.8090303@imm.ox.ac.uk> Message-ID: <4D3D6663.1090402@ebi.ac.uk> On 24/01/11 11:09, Stephen Taylor wrote: > Hi again Peter, > >> On 01/20/11 09:17, Stephen Taylor wrote: >> >>> Is there a bug in the gff3 output of fuzznuc? >>> >>> ##gff-version 3 >>> ##sequence-region chr21 1 46944323 >>> #!Date 2011-01-20 >>> #!Type DNA >>> #!Source-version EMBOSS 6.3.1 >>> chr21 fuzznuc nucleotide_motif 13362906 13362942 37.000 + . >>> ID="chr21.1";note="*pat pattern" >>> >>> It would be nice to actually show the pattern matched in the note field. >> >> or both. What it shows is the "name" of the pattern, which usually >> defaults to pattern. > > Please can you define 'usually' i.e. What are the 'rules' for getting it > to show the pattern? Usual behaviour when I run it, is it shows > note="*pat pattern". The pattern name defaults to 'pattern'. This will always be the case when the user specifies a pattern on the command line with no other options. Where multiple patterns are defined in an input file ('filename syntax for the pattern), each has a unique name in the file. The pattern name can also be set via the -pname qualifier. So it makes sense to include the pattern string in the qualifier value, and to rename it to "Pattern" in the report output. regards, Peter From stephen.taylor at imm.ox.ac.uk Mon Jan 24 06:56:52 2011 From: stephen.taylor at imm.ox.ac.uk (Stephen Taylor) Date: Mon, 24 Jan 2011 11:56:52 +0000 Subject: [EMBOSS] SAM format In-Reply-To: <4D3D6663.1090402@ebi.ac.uk> References: <4D370C9D.5080902@imm.ox.ac.uk> <4D37EF67.1080206@ebi.ac.uk> <4D37FDB9.7000804@imm.ox.ac.uk> <4D380313.7030106@ebi.ac.uk> <4D3D5DD1.8090303@imm.ox.ac.uk> <4D3D6663.1090402@ebi.ac.uk> Message-ID: <4D3D6904.6050604@imm.ox.ac.uk> On 24/01/2011 11:45, Peter Rice wrote: > On 24/01/11 11:09, Stephen Taylor wrote: >> Hi again Peter, >> >>> On 01/20/11 09:17, Stephen Taylor wrote: >>> >>>> Is there a bug in the gff3 output of fuzznuc? >>>> >>>> ##gff-version 3 >>>> ##sequence-region chr21 1 46944323 >>>> #!Date 2011-01-20 >>>> #!Type DNA >>>> #!Source-version EMBOSS 6.3.1 >>>> chr21 fuzznuc nucleotide_motif 13362906 13362942 37.000 + . >>>> ID="chr21.1";note="*pat pattern" >>>> >>>> It would be nice to actually show the pattern matched in the note field. >>> >>> or both. What it shows is the "name" of the pattern, which usually >>> defaults to pattern. >> >> Please can you define 'usually' i.e. What are the 'rules' for getting it >> to show the pattern? Usual behaviour when I run it, is it shows >> note="*pat pattern". > > The pattern name defaults to 'pattern'. This will always be the case > when the user specifies a pattern on the command line with no other options. > > Where multiple patterns are defined in an input file ('filename syntax > for the pattern), each has a unique name in the file. > > The pattern name can also be set via the -pname qualifier. > > So it makes sense to include the pattern string in the qualifier value, > and to rename it to "Pattern" in the report output. > I see. Many thanks for clearing that up. Steve From stephen.taylor at imm.ox.ac.uk Tue Jan 25 05:03:14 2011 From: stephen.taylor at imm.ox.ac.uk (Stephen Taylor) Date: Tue, 25 Jan 2011 10:03:14 +0000 Subject: [EMBOSS] GFF no header Message-ID: <4D3E9FE2.4090008@imm.ox.ac.uk> Hi, I seem to remember there was an option in EMBOSS that returned a GFF3 report format without its '#' header. Please can somebody remind me what it is? Thanks a lot, Steve From wo.granon at gmail.com Wed Jan 26 03:13:27 2011 From: wo.granon at gmail.com (Wolfgang Gruber) Date: Wed, 26 Jan 2011 09:13:27 +0100 Subject: [EMBOSS] Retrieve data from entrez Message-ID: Hello, i am not sure if I did it the right way. I wanted to access the entrez database, because in general I get my sequences from there. I putted this entry into my emboss.default: DB entrez [ type: N format: genbank method: entrez fields: "id acc gi sv des org key" url: "http://www.ncbi.nlm.nih.gov/sites/gquery" ] Then i tried to retrieve the data with the entrez id. In most cases this works, in some not. For example seqret entrez:NM_000527 works, but seqret entrez:NP_000518 does not: "Error: Unable to read sequence 'entrez:NP_000518'" Can you help me what I did wrong? Ones more what I want: I want to give the entrez id and retrieve then the corresponding sequence. Thanks, Wolfgang From david.bauer at bayer.com Wed Jan 26 03:39:28 2011 From: david.bauer at bayer.com (david.bauer at bayer.com) Date: Wed, 26 Jan 2011 09:39:28 +0100 Subject: [EMBOSS] Antwort: Retrieve data from entrez In-Reply-To: Message-ID: Hi, the entrez method looks at the type (N or P) to formulate the eutils request to the ncbi server. As NP_ is a protein sequence, the database specified in the request must be protein and not nucleotide. So you need two separate entries in emboss.default for nucleotide and protein sequences. David. emboss-bounces at lists.open-bio.org schrieb am 26/01/2011 09:13:27: > Hello, > > i am not sure if I did it the right way. I wanted to access the entrez > database, because in general I get my sequences from there. I putted > this entry into my emboss.default: > > DB entrez [ > type: N > format: genbank > method: entrez > fields: "id acc gi sv des org key" > url: "http://www.ncbi.nlm.nih.gov/sites/gquery" > ] > > Then i tried to retrieve the data with the entrez id. In most cases > this works, in some not. For example seqret entrez:NM_000527 works, > but seqret entrez:NP_000518 does not: "Error: Unable to read sequence > 'entrez:NP_000518'" > > Can you help me what I did wrong? > > Ones more what I want: I want to give the entrez id and retrieve then > the corresponding sequence. > > Thanks, > Wolfgang > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss From hrh at fmi.ch Wed Jan 26 03:49:42 2011 From: hrh at fmi.ch (Hans-Rudolf Hotz) Date: Wed, 26 Jan 2011 09:49:42 +0100 Subject: [EMBOSS] Retrieve data from entrez In-Reply-To: References: Message-ID: <4D3FE026.4010502@fmi.ch> Hi Wolfgang 'NP_000518' is a protein entry. You can fetch it by adding a second database definition (with "type: P"), ie: DB entrezP [ type: P format: genbank method: entrez fields: "id acc gi sv des org key" url: "http://www.ncbi.nlm.nih.gov/sites/gquery" ] and then you can fetch the protein sequence: -bash-3.2$ seqret entrezP:NP_000518 -auto stdout |head -3 >NP_000518 NP_000518.1 low-density lipoprotein receptor isoform 1 precursor [Homo sapiens]. mgpwgwklrwtvalllaaagtavgdrcernefqcqdgkcisykwvcdgsaecqdgsdesq etclsvtcksgdfscggrvnrcipqfwrcdgqvdcdngsdeqgcppktcsqdefrchdgk -bash-3.2$ Regards, Hans On 01/26/2011 09:13 AM, Wolfgang Gruber wrote: > Hello, > > i am not sure if I did it the right way. I wanted to access the entrez > database, because in general I get my sequences from there. I putted > this entry into my emboss.default: > > DB entrez [ > type: N > format: genbank > method: entrez > fields: "id acc gi sv des org key" > url: "http://www.ncbi.nlm.nih.gov/sites/gquery" > ] > > Then i tried to retrieve the data with the entrez id. In most cases > this works, in some not. For example seqret entrez:NM_000527 works, > but seqret entrez:NP_000518 does not: "Error: Unable to read sequence > 'entrez:NP_000518'" > > Can you help me what I did wrong? > > Ones more what I want: I want to give the entrez id and retrieve then > the corresponding sequence. > > Thanks, > Wolfgang > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss From wo.granon at gmail.com Wed Jan 26 04:47:31 2011 From: wo.granon at gmail.com (Wolfgang Gruber) Date: Wed, 26 Jan 2011 10:47:31 +0100 Subject: [EMBOSS] Retrieve data from entrez In-Reply-To: <4D3FE026.4010502@fmi.ch> References: <4D3FE026.4010502@fmi.ch> Message-ID: I understand. Thank you very much! I didn't recognize the type switch. In general: Is this way ok to get the Sequences behind an entrez id? Or is there a more specific way? Because this way I can also specify a search term and then I get more than one result. Thanks, Wolfgang 2011/1/26 Hans-Rudolf Hotz : > Hi Wolfgang > > 'NP_000518' is a protein entry. You can fetch it by adding a second database > definition (with "type: P"), ie: > > > DB entrezP [ > ? ? ? ? type: P > ? ? ? ? format: genbank > ? ? ? ? method: entrez > ? ? ? ? fields: "id acc gi sv des org key" > ? ? ? ? url: ? ?"http://www.ncbi.nlm.nih.gov/sites/gquery" > ] > > > and then you can fetch the protein sequence: > > > -bash-3.2$ seqret entrezP:NP_000518 -auto stdout |head -3 >>NP_000518 NP_000518.1 low-density lipoprotein receptor isoform 1 precursor >> [Homo sapiens]. > mgpwgwklrwtvalllaaagtavgdrcernefqcqdgkcisykwvcdgsaecqdgsdesq > etclsvtcksgdfscggrvnrcipqfwrcdgqvdcdngsdeqgcppktcsqdefrchdgk > -bash-3.2$ > > > Regards, Hans > > > > On 01/26/2011 09:13 AM, Wolfgang Gruber wrote: >> >> Hello, >> >> i am not sure if I did it the right way. I wanted to access the entrez >> database, because in general I get my sequences from there. I putted >> this entry into my emboss.default: >> >> DB entrez [ >> ? ? ? ? ?type: N >> ? ? ? ? ?format: genbank >> ? ? ? ? ?method: entrez >> ? ? ? ? ?fields: "id acc gi sv des org key" >> ? ? ? ? ?url: ? ?"http://www.ncbi.nlm.nih.gov/sites/gquery" >> ] >> >> Then i tried to retrieve the data with the entrez id. In most cases >> this works, in some not. For example seqret entrez:NM_000527 works, >> but seqret entrez:NP_000518 does not: "Error: Unable to read sequence >> 'entrez:NP_000518'" >> >> Can you help me what I did wrong? >> >> Ones more what I want: I want to give the entrez id and retrieve then >> the corresponding sequence. >> >> Thanks, >> Wolfgang >> _______________________________________________ >> EMBOSS mailing list >> EMBOSS at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/emboss > From Lionel.Brooks at dartmouth.edu Thu Jan 27 18:02:42 2011 From: Lionel.Brooks at dartmouth.edu (Lionel (Lee) Brooks 3rd) Date: Thu, 27 Jan 2011 18:02:42 -0500 Subject: [EMBOSS] dreg: does it search both strands? Message-ID: <4D41F992.5030900@dartmouth.edu> Hello fellow EMBOSS fans, I am using the dreg program to search the human genome for my favorite motif. I was unable to find any information regarding the meaning of the strand information in the output. Does dreg search both strands or will it always return "+" as the strand designation of the hits that it finds? Thanks for your continued support and development of this fantastic tool! Sincerely, Lionel "Lee" Brooks 3rd Dartmouth Genetics Grad Student From robin at hms.harvard.edu Fri Jan 28 14:51:27 2011 From: robin at hms.harvard.edu (Robin Colgrove) Date: Fri, 28 Jan 2011 14:51:27 -0500 Subject: [EMBOSS] Batch alignments? In-Reply-To: <4D41F992.5030900@dartmouth.edu> References: <4D41F992.5030900@dartmouth.edu> Message-ID: Hello EMBOSS-folk. Given a set of fasta files, each an ordered list of coding sequences for a set of highly homologous (viral) genomes, is there some straightforward way of generating a file with alignments of the coding sequences other than doing each one manually (around a 100 genes). That is, if each file is of the form: >gene1 ATG... ...TAG >gene2 ATG... ...TAA etc.... I want to align each set of homologous genes. I've used matcher and needle to do a gene at a time, but it would be nice to batch this. thanks, Robin Colgrove Harvard Medical School PS: Embarrassingly enough, I am using v3.0.0 of emboss (Mac OS X 10.6.5). Can I just install a new version or do I have to uninstall everything first? Looking for the minimum fuss route. From db60 at st-andrews.ac.uk Sat Jan 29 07:08:34 2011 From: db60 at st-andrews.ac.uk (Daniel Barker) Date: Sat, 29 Jan 2011 12:08:34 +0000 Subject: [EMBOSS] Batch alignments? In-Reply-To: References: <4D41F992.5030900@dartmouth.edu> Message-ID: <4D440342.8060703@st-andrews.ac.uk> Dear Robin, In a Perl script, you could read your sequences using BioPerl Seq::IO, create input files, and execute the EMBOSS commands from Perl with system() or `...`. Remember to close temporary files you've created in Perl before using them - this forces the last bit of the file to be really written, rather than stay languishing in some buffer. This is just one suggestion - there will be other ways. An excellent guide to Perl is at: http://korflab.ucdavis.edu/Unix_and_Perl If I remember, some earlier version of needle had a bug which could affect scores. So you might want to upgrade. For coding sequences, consider doing the alignment at the protein level - unless there's a good reason not to. I.e. translate your coding sequences (perhaps with EMBOSS transeq) and align the translations. Generally, this will be more sensitive and less easily misled. If you require nucleotide alignment, you can convert back to the original nucleotides afterwards - but this is more likely to be required with multiple alignment than with pairwise (and for multiple alignments can be achieved with EMBOSS tranalign). Best regards, Daniel -- Daniel Barker http://bio.st-andrews.ac.uk/staff/db60.htm The University of St Andrews is a charity registered in Scotland : No SC013532 From jmeador45 at mac.com Sun Jan 30 23:49:38 2011 From: jmeador45 at mac.com (Jim Meador) Date: Sun, 30 Jan 2011 23:49:38 -0500 Subject: [EMBOSS] can't install emboss 6.3.1 in mac os x 10.6 Message-ID: <0192CFFE-D4EB-4FDB-B09D-59AB292ED208@mac.com> Hi Everyone, I am wanting to pgrade EMBOSS 6.3.1 on Mac OS X 10.6.6 (MacBook Pro 2.2 GHz, 4GB) from EMBOSS 6.2.0 that was installed in Leopoard (10.5) before I upgraded to Snow Leopard (10.6) and it seems to not do the make process correctly, where in the plplot directory, the .libs directory does not get created, so when I do sudo make install, it fails with these error messages: Making install in plplot make[1]: Entering directory `/Users/jmeador/newApps/MolBioChemSoftware/MolBioGeneral/EMBOSS/EMBOSS-6.3.1/plplot' Making install in lib make[2]: Entering directory `/Users/jmeador/newApps/MolBioChemSoftware/MolBioGeneral/EMBOSS/EMBOSS-6.3.1/plplot/lib' make[3]: Entering directory `/Users/jmeador/newApps/MolBioChemSoftware/MolBioGeneral/EMBOSS/EMBOSS-6.3.1/plplot/lib' make[3]: Nothing to be done for `install-exec-am'. test -z "/usr/local/share/EMBOSS" || ../.././install-sh -c -d "/usr/local/share/EMBOSS" /usr/bin/install -c -m 644 plstnd5.fnt plxtnd5.fnt '/usr/local/share/EMBOSS' make[3]: Leaving directory `/Users/jmeador/newApps/MolBioChemSoftware/MolBioGeneral/EMBOSS/EMBOSS-6.3.1/plplot/lib' make[2]: Leaving directory `/Users/jmeador/newApps/MolBioChemSoftware/MolBioGeneral/EMBOSS/EMBOSS-6.3.1/plplot/lib' make[2]: Entering directory `/Users/jmeador/newApps/MolBioChemSoftware/MolBioGeneral/EMBOSS/EMBOSS-6.3.1/plplot' make[3]: Entering directory `/Users/jmeador/newApps/MolBioChemSoftware/MolBioGeneral/EMBOSS/EMBOSS-6.3.1/plplot' test -z "/usr/local/lib" || .././install-sh -c -d "/usr/local/lib" /bin/sh ../libtool --mode=install /usr/bin/install -c libeplplot.la '/usr/local/lib' libtool: install: /usr/bin/install -c .libs/libeplplot.3.dylib /usr/local/lib/libeplplot.3.dylib install: .libs/libeplplot.3.dylib: No such file or directory make[3]: *** [install-libLTLIBRARIES] Error 71 make[3]: Leaving directory `/Users/jmeador/newApps/MolBioChemSoftware/MolBioGeneral/EMBOSS/EMBOSS-6.3.1/plplot' make[2]: *** [install-am] Error 2 make[2]: Leaving directory `/Users/jmeador/newApps/MolBioChemSoftware/MolBioGeneral/EMBOSS/EMBOSS-6.3.1/plplot' make[1]: *** [install-recursive] Error 1 make[1]: Leaving directory `/Users/jmeador/newApps/MolBioChemSoftware/MolBioGeneral/EMBOSS/EMBOSS-6.3.1/plplot' make: *** [install-recursive] Error 1 When I look in the source directory, /EMBOSS-6.3.1/plplot/ there is no .libs directory as there is in another installation on a newer MacBook Pro that I was able to successfully install this same software (10.6.6, 2.6 GHz, 8GB). My setup is a little more complicated than I would like, since I have installed the eBiotools-3.0.1-leopard software which sets up an older version of emboss 5.0.0 within a /usr/ebiotools/ directory and uses a very nice gui program to access these older emboss programs, called "eBioX" (and I don't want to lose this). So I have been installing the newer 6.x version of emboss to use at the commandline and with kemboss, both of which work, sort of. I have to play with the environment variables to get the text output programs to work, but I cannot get the graphics to work from various emboss programs that try to make graphs, such as "charge". The text-based programs work but I want to get the graphics working as well as it does from the ebiotools versions and will probably need to re-make emboss 6.3.1 after (re)installing gd and libpng. However, on this mac, neither ps nor x11 work. On the newer mac, with 6.3.1 installed, I don't have png or gif support, but I can at least get graphs in ps and x11 to work. Does anyone have any ideas of what I may be doing wrong? Is it possible that some environment variable could be causing this? Any ideas will be greatly appreciated. Thanks, Jim From idrummon at receptor.mgh.harvard.edu Mon Jan 31 11:05:06 2011 From: idrummon at receptor.mgh.harvard.edu (Iain Drummond) Date: Mon, 31 Jan 2011 11:05:06 -0500 Subject: [EMBOSS] can't install emboss 6.3.1 in mac os x 10.6 In-Reply-To: <0192CFFE-D4EB-4FDB-B09D-59AB292ED208@mac.com> Message-ID: I seem to remember that i could bypass this issue by configuring EMBOSS to install without x11. I realize that's not what you want to do. I think the problem stems from the directory structure Apple uses for x11; i.e. Its not where EMBOSS thinks it is. Maybe Apple put xll in a new place with 10.6? Iain Drummond On 1/30/11 11:49 PM, "Jim Meador" wrote: > Hi Everyone, > > I am wanting to pgrade EMBOSS 6.3.1 on Mac OS X 10.6.6 (MacBook Pro 2.2 GHz, > 4GB) from EMBOSS 6.2.0 that was installed in Leopoard (10.5) before I upgraded > to Snow Leopard (10.6) and it seems to not do the make process correctly, > where in the plplot directory, the .libs directory does not get created, so > when I do sudo make install, it fails with these error messages: > > Making install in plplot > make[1]: Entering directory > `/Users/jmeador/newApps/MolBioChemSoftware/MolBioGeneral/EMBOSS/EMBOSS-6.3.1/p > lplot' > Making install in lib > make[2]: Entering directory > `/Users/jmeador/newApps/MolBioChemSoftware/MolBioGeneral/EMBOSS/EMBOSS-6.3.1/p > lplot/lib' > make[3]: Entering directory > `/Users/jmeador/newApps/MolBioChemSoftware/MolBioGeneral/EMBOSS/EMBOSS-6.3.1/p > lplot/lib' > make[3]: Nothing to be done for `install-exec-am'. > test -z "/usr/local/share/EMBOSS" || ../.././install-sh -c -d > "/usr/local/share/EMBOSS" > /usr/bin/install -c -m 644 plstnd5.fnt plxtnd5.fnt '/usr/local/share/EMBOSS' > make[3]: Leaving directory > `/Users/jmeador/newApps/MolBioChemSoftware/MolBioGeneral/EMBOSS/EMBOSS-6.3.1/p > lplot/lib' > make[2]: Leaving directory > `/Users/jmeador/newApps/MolBioChemSoftware/MolBioGeneral/EMBOSS/EMBOSS-6.3.1/p > lplot/lib' > make[2]: Entering directory > `/Users/jmeador/newApps/MolBioChemSoftware/MolBioGeneral/EMBOSS/EMBOSS-6.3.1/p > lplot' > make[3]: Entering directory > `/Users/jmeador/newApps/MolBioChemSoftware/MolBioGeneral/EMBOSS/EMBOSS-6.3.1/p > lplot' > test -z "/usr/local/lib" || .././install-sh -c -d "/usr/local/lib" > /bin/sh ../libtool --mode=install /usr/bin/install -c libeplplot.la > '/usr/local/lib' > libtool: install: /usr/bin/install -c .libs/libeplplot.3.dylib > /usr/local/lib/libeplplot.3.dylib > install: .libs/libeplplot.3.dylib: No such file or directory > make[3]: *** [install-libLTLIBRARIES] Error 71 > make[3]: Leaving directory > `/Users/jmeador/newApps/MolBioChemSoftware/MolBioGeneral/EMBOSS/EMBOSS-6.3.1/p > lplot' > make[2]: *** [install-am] Error 2 > make[2]: Leaving directory > `/Users/jmeador/newApps/MolBioChemSoftware/MolBioGeneral/EMBOSS/EMBOSS-6.3.1/p > lplot' > make[1]: *** [install-recursive] Error 1 > make[1]: Leaving directory > `/Users/jmeador/newApps/MolBioChemSoftware/MolBioGeneral/EMBOSS/EMBOSS-6.3.1/p > lplot' > make: *** [install-recursive] Error 1 > > When I look in the source directory, /EMBOSS-6.3.1/plplot/ there is no .libs > directory as there is in another installation on a newer MacBook Pro that I > was able to successfully install this same software (10.6.6, 2.6 GHz, 8GB). > > My setup is a little more complicated than I would like, since I have > installed the eBiotools-3.0.1-leopard software which sets up an older version > of emboss 5.0.0 within a /usr/ebiotools/ directory and uses a very nice gui > program to access these older emboss programs, called "eBioX" (and I don't > want to lose this). So I have been installing the newer 6.x version of emboss > to use at the commandline and with kemboss, both of which work, sort of. I > have to play with the environment variables to get the text output programs to > work, but I cannot get the graphics to work from various emboss programs that > try to make graphs, such as "charge". The text-based programs work but I want > to get the graphics working as well as it does from the ebiotools versions and > will probably need to re-make emboss 6.3.1 after (re)installing gd and libpng. > However, on this mac, neither ps nor x11 work. On the newer mac, with 6.3.1 > installed, I don't have png or gif support, but I can at least get g! > raphs in ps and x11 to work. > > Does anyone have any ideas of what I may be doing wrong? Is it possible that > some environment variable could be causing this? > > Any ideas will be greatly appreciated. > Thanks, > Jim > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. From frank.foerster at biozentrum.uni-wuerzburg.de Mon Jan 31 13:03:16 2011 From: frank.foerster at biozentrum.uni-wuerzburg.de (=?ISO-8859-15?Q?Frank_F=F6rster?=) Date: Mon, 31 Jan 2011 19:03:16 +0100 Subject: [EMBOSS] Batch alignments? Message-ID: <4D46F964.4010705@biozentrum.uni-wuerzburg.de> Dear Robin, Starting with release 6.2 the program needleall is included into the EMBOSS software package. This program allows the generation of all vs. all alignments of two sequence sets. So you can generate all alignments with just one program. See http://emboss.sourceforge.net/apps/release/6.3/emboss/apps/needleall.html for more information. The best thing about needleall is you do not need to write a Perl script, no matter if this is just a simple script. Maybe this can help you to find arguments for upgrading to a newer EMBOSS release. Best regards, Frank -- Dr. rer. net. Dipl. Biochem. Frank F?rster Department of Bioinformatics University of W?rzburg, Germany Fon: +49 931 - 31 84555 Fax: +49 931 - 31 84552 frank.foerster at biozentrum.uni-wuerzburg.de From jmeador45 at mac.com Mon Jan 31 22:43:50 2011 From: jmeador45 at mac.com (Jim Meador) Date: Mon, 31 Jan 2011 22:43:50 -0500 Subject: [EMBOSS] can't install emboss 6.3.1 in mac os x 10.6 In-Reply-To: References: Message-ID: <2D54C5BB-C798-43C5-8EBA-2CCC9DEEC740@mac.com> Hi Iain, I think you have the right idea. I had installed XQuartz which actually fixed some other issues I was having (but created new ones ;-) and I think I need to re-configure with x11=/opt/x11 or something like that. So I think you have the answer and thank you for the help. Sincerely, Jim (just around the corner in Cambridge) On Jan 31, 2011, at 11:05 AM, Iain Drummond wrote: > I seem to remember that i could bypass this issue by configuring EMBOSS to > install without x11. I realize that's not what you want to do. I think the > problem stems from the directory structure Apple uses for x11; i.e. Its not > where EMBOSS thinks it is. Maybe Apple put xll in a new place with 10.6? > > Iain Drummond > > > On 1/30/11 11:49 PM, "Jim Meador" wrote: > >> Hi Everyone, >> >> I am wanting to pgrade EMBOSS 6.3.1 on Mac OS X 10.6.6 (MacBook Pro 2.2 GHz, >> 4GB) from EMBOSS 6.2.0 that was installed in Leopoard (10.5) before I upgraded >> to Snow Leopard (10.6) and it seems to not do the make process correctly, >> where in the plplot directory, the .libs directory does not get created, so >> when I do sudo make install, it fails with these error messages: >> >> Making install in plplot >> make[1]: Entering directory >> `/Users/jmeador/newApps/MolBioChemSoftware/MolBioGeneral/EMBOSS/EMBOSS-6.3.1/p >> lplot' >> Making install in lib >> make[2]: Entering directory >> `/Users/jmeador/newApps/MolBioChemSoftware/MolBioGeneral/EMBOSS/EMBOSS-6.3.1/p >> lplot/lib' >> make[3]: Entering directory >> `/Users/jmeador/newApps/MolBioChemSoftware/MolBioGeneral/EMBOSS/EMBOSS-6.3.1/p >> lplot/lib' >> make[3]: Nothing to be done for `install-exec-am'. >> test -z "/usr/local/share/EMBOSS" || ../.././install-sh -c -d >> "/usr/local/share/EMBOSS" >> /usr/bin/install -c -m 644 plstnd5.fnt plxtnd5.fnt '/usr/local/share/EMBOSS' >> make[3]: Leaving directory >> `/Users/jmeador/newApps/MolBioChemSoftware/MolBioGeneral/EMBOSS/EMBOSS-6.3.1/p >> lplot/lib' >> make[2]: Leaving directory >> `/Users/jmeador/newApps/MolBioChemSoftware/MolBioGeneral/EMBOSS/EMBOSS-6.3.1/p >> lplot/lib' >> make[2]: Entering directory >> `/Users/jmeador/newApps/MolBioChemSoftware/MolBioGeneral/EMBOSS/EMBOSS-6.3.1/p >> lplot' >> make[3]: Entering directory >> `/Users/jmeador/newApps/MolBioChemSoftware/MolBioGeneral/EMBOSS/EMBOSS-6.3.1/p >> lplot' >> test -z "/usr/local/lib" || .././install-sh -c -d "/usr/local/lib" >> /bin/sh ../libtool --mode=install /usr/bin/install -c libeplplot.la >> '/usr/local/lib' >> libtool: install: /usr/bin/install -c .libs/libeplplot.3.dylib >> /usr/local/lib/libeplplot.3.dylib >> install: .libs/libeplplot.3.dylib: No such file or directory >> make[3]: *** [install-libLTLIBRARIES] Error 71 >> make[3]: Leaving directory >> `/Users/jmeador/newApps/MolBioChemSoftware/MolBioGeneral/EMBOSS/EMBOSS-6.3.1/p >> lplot' >> make[2]: *** [install-am] Error 2 >> make[2]: Leaving directory >> `/Users/jmeador/newApps/MolBioChemSoftware/MolBioGeneral/EMBOSS/EMBOSS-6.3.1/p >> lplot' >> make[1]: *** [install-recursive] Error 1 >> make[1]: Leaving directory >> `/Users/jmeador/newApps/MolBioChemSoftware/MolBioGeneral/EMBOSS/EMBOSS-6.3.1/p >> lplot' >> make: *** [install-recursive] Error 1 >> >> When I look in the source directory, /EMBOSS-6.3.1/plplot/ there is no .libs >> directory as there is in another installation on a newer MacBook Pro that I >> was able to successfully install this same software (10.6.6, 2.6 GHz, 8GB). >> >> My setup is a little more complicated than I would like, since I have >> installed the eBiotools-3.0.1-leopard software which sets up an older version >> of emboss 5.0.0 within a /usr/ebiotools/ directory and uses a very nice gui >> program to access these older emboss programs, called "eBioX" (and I don't >> want to lose this). So I have been installing the newer 6.x version of emboss >> to use at the commandline and with kemboss, both of which work, sort of. I >> have to play with the environment variables to get the text output programs to >> work, but I cannot get the graphics to work from various emboss programs that >> try to make graphs, such as "charge". The text-based programs work but I want >> to get the graphics working as well as it does from the ebiotools versions and >> will probably need to re-make emboss 6.3.1 after (re)installing gd and libpng. >> However, on this mac, neither ps nor x11 work. On the newer mac, with 6.3.1 >> installed, I don't have png or gif support, but I can at least get g! >> raphs in ps and x11 to work. >> >> Does anyone have any ideas of what I may be doing wrong? Is it possible that >> some environment variable could be causing this? >> >> Any ideas will be greatly appreciated. >> Thanks, >> Jim >> _______________________________________________ >> EMBOSS mailing list >> EMBOSS at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/emboss >> > > > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and properly > dispose of the e-mail. > From Lionel.Brooks at dartmouth.edu Wed Jan 5 18:46:08 2011 From: Lionel.Brooks at dartmouth.edu (Lionel (Lee) Brooks 3rd) Date: Wed, 05 Jan 2011 13:46:08 -0500 Subject: [EMBOSS] dbifasta error "too many parameters" Message-ID: <4D24BC70.2000901@dartmouth.edu> Hello Gentlepeople, I am interested in using regular expressions to search the human genome for occurrences of my favorite motif. I need coordinate values for each hit. I chose the EMBOSS program "dreg" for this task. I have a set of of fasta files; I have one fasta file per human chromosome. I wish to index these files with dbifasta so that I can use the dreg program for the regex search. I use the following command: me at mycpu$ dbifasta -dbname UCSC_hg19_softmask -idformat simple -directory /storage/EMBOSS/Emboss_DB -filenames *.fa -release hg19 -date 01/04/11 -outfile /storage/EMBOSS/Emboss_DB/logfile.dbifasta And receive the following error: Error: Argument 'seq01' : Too many parameters 2/1 ...the file that holds the chromosome sequences are named seq00.fa, seq01.fa, seq02.fa ... so on. Any sort of help is greatly appreciated. Thank you for your time in developing and maintaining this resource! -Lionel Brooks III Genetics Grad Student Dartmouth College From pmr at ebi.ac.uk Thu Jan 6 00:09:52 2011 From: pmr at ebi.ac.uk (Peter Rice) Date: Thu, 06 Jan 2011 00:09:52 +0000 Subject: [EMBOSS] dbifasta error "too many parameters" In-Reply-To: <4D24BC70.2000901@dartmouth.edu> References: <4D24BC70.2000901@dartmouth.edu> Message-ID: <4D250850.6060408@ebi.ac.uk> On 05/01/2011 18:46, Lionel (Lee) Brooks 3rd wrote: > I use the following command: > > me at mycpu$ dbifasta -dbname UCSC_hg19_softmask -idformat simple > -directory /storage/EMBOSS/Emboss_DB -filenames *.fa -release hg19 -date > 01/04/11 -outfile /storage/EMBOSS/Emboss_DB/logfile.dbifasta > > And receive the following error: > > Error: Argument 'seq01' : Too many parameters 2/1 > > ...the file that holds the chromosome sequences are named seq00.fa, > seq01.fa, seq02.fa ... so on. > Any sort of help is greatly appreciated. This is one of those Unix command line issues ... you need quotes around the "*.fa" (single or double quotes will do). The shell expands *.fa into the list of filenames before EMBOSS sees the results, and the second one is your "extra parameter". regards, Peter Rice EMBOSS team From wo.granon at gmail.com Wed Jan 12 17:16:14 2011 From: wo.granon at gmail.com (wo.granon at gmail.com) Date: Wed, 12 Jan 2011 18:16:14 +0100 Subject: [EMBOSS] error while loading shared libraries: libnucleus.so.6 Message-ID: Hello, I installed stable EMBOSS 6.3.1 on OpenSuse 11.3. ./configure, make and make install ran without an error. But when I try to run an EMBOSS app, i get the following error: # embossversion embossversion: error while loading shared libraries: libnucleus.so.6: cannot open shared object file: No such file or directory I think the attached output could help. Does anyone know what is wrong with my installation? Do you need additional data? Thanks, Wolfgang # ldd $(which embossversion) linux-gate.so.1 => (0xffffe000) libnucleus.so.6 => not found libacd.so.6 => not found libajaxdb.so.6 => not found libensembl.so.6 => not found libajaxg.so.6 => not found libajax.so.6 => not found libezlib.so.1 => not found libeexpat.so.1 => not found libepcre.so.7 => not found libeplplot.so.3 => not found libpq.so.5 => /usr/lib/libpq.so.5 (0xb77a4000) libX11.so.6 => /usr/lib/libX11.so.6 (0xb7669000) libgd.so.2 => /usr/lib/libgd.so.2 (0xb7622000) libpng14.so.14 => /usr/lib/libpng14.so.14 (0xb75f6000) libz.so.1 => /lib/libz.so.1 (0xb75e1000) libm.so.6 => /lib/libm.so.6 (0xb75b7000) libc.so.6 => /lib/libc.so.6 (0xb744c000) libssl.so.1.0.0 => /lib/libssl.so.1.0.0 (0xb73f5000) libcrypto.so.1.0.0 => /lib/libcrypto.so.1.0.0 (0xb7255000) libkrb5.so.3 => /usr/lib/libkrb5.so.3 (0xb718d000) libcom_err.so.2 => /lib/libcom_err.so.2 (0xb7187000) libgssapi_krb5.so.2 => /usr/lib/libgssapi_krb5.so.2 (0xb7150000) libldap_r-2.4.so.2 => /usr/lib/libldap_r-2.4.so.2 (0xb7100000) libpthread.so.0 => /lib/libpthread.so.0 (0xb70e5000) libxcb.so.1 => /usr/lib/libxcb.so.1 (0xb70c5000) libdl.so.2 => /lib/libdl.so.2 (0xb70bf000) libXpm.so.4 => /usr/lib/libXpm.so.4 (0xb70ac000) libjpeg.so.8 => /usr/lib/libjpeg.so.8 (0xb7073000) libfontconfig.so.1 => /usr/lib/libfontconfig.so.1 (0xb703d000) libfreetype.so.6 => /usr/lib/libfreetype.so.6 (0xb6fb6000) /lib/ld-linux.so.2 (0xb77e3000) libk5crypto.so.3 => /usr/lib/libk5crypto.so.3 (0xb6f8d000) libkrb5support.so.0 => /usr/lib/libkrb5support.so.0 (0xb6f84000) libkeyutils.so.1 => /lib/libkeyutils.so.1 (0xb6f80000) libresolv.so.2 => /lib/libresolv.so.2 (0xb6f69000) liblber-2.4.so.2 => /usr/lib/liblber-2.4.so.2 (0xb6f59000) libsasl2.so.2 => /usr/lib/libsasl2.so.2 (0xb6f3d000) libXau.so.6 => /usr/lib/libXau.so.6 (0xb6f39000) libexpat.so.1 => /lib/libexpat.so.1 (0xb6f0f000) From ajb at ebi.ac.uk Wed Jan 12 17:37:05 2011 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Wed, 12 Jan 2011 17:37:05 -0000 (UTC) Subject: [EMBOSS] error while loading shared libraries: libnucleus.so.6 In-Reply-To: References: Message-ID: <51851.86.26.12.63.1294853825.squirrel@webmail.ebi.ac.uk> Hello Wolfgang, On OpenSuse that error usually means you've installed EMBOSS into /usr/local such that the libraries are in /usr/local/lib. That library directory is cached on OpenSuse so all you should need to do is, with privilege, type "/sbin/ldconfig" to rebuild the cache. HTH Alan > Hello, > > I installed stable EMBOSS 6.3.1 on OpenSuse 11.3. > > ./configure, make and make install ran without an error. But when I > try to run an EMBOSS app, i get the following error: > > # embossversion > embossversion: error while loading shared libraries: libnucleus.so.6: > cannot open shared object file: No such file or directory > > I think the attached output could help. Does anyone know what is wrong > with my installation? Do you need additional data? > > Thanks, > Wolfgang > > # ldd $(which embossversion) > linux-gate.so.1 => (0xffffe000) > libnucleus.so.6 => not found > libacd.so.6 => not found > libajaxdb.so.6 => not found > libensembl.so.6 => not found > libajaxg.so.6 => not found > libajax.so.6 => not found > libezlib.so.1 => not found > libeexpat.so.1 => not found > libepcre.so.7 => not found > libeplplot.so.3 => not found > libpq.so.5 => /usr/lib/libpq.so.5 (0xb77a4000) > libX11.so.6 => /usr/lib/libX11.so.6 (0xb7669000) > libgd.so.2 => /usr/lib/libgd.so.2 (0xb7622000) > libpng14.so.14 => /usr/lib/libpng14.so.14 (0xb75f6000) > libz.so.1 => /lib/libz.so.1 (0xb75e1000) > libm.so.6 => /lib/libm.so.6 (0xb75b7000) > libc.so.6 => /lib/libc.so.6 (0xb744c000) > libssl.so.1.0.0 => /lib/libssl.so.1.0.0 (0xb73f5000) > libcrypto.so.1.0.0 => /lib/libcrypto.so.1.0.0 (0xb7255000) > libkrb5.so.3 => /usr/lib/libkrb5.so.3 (0xb718d000) > libcom_err.so.2 => /lib/libcom_err.so.2 (0xb7187000) > libgssapi_krb5.so.2 => /usr/lib/libgssapi_krb5.so.2 (0xb7150000) > libldap_r-2.4.so.2 => /usr/lib/libldap_r-2.4.so.2 (0xb7100000) > libpthread.so.0 => /lib/libpthread.so.0 (0xb70e5000) > libxcb.so.1 => /usr/lib/libxcb.so.1 (0xb70c5000) > libdl.so.2 => /lib/libdl.so.2 (0xb70bf000) > libXpm.so.4 => /usr/lib/libXpm.so.4 (0xb70ac000) > libjpeg.so.8 => /usr/lib/libjpeg.so.8 (0xb7073000) > libfontconfig.so.1 => /usr/lib/libfontconfig.so.1 (0xb703d000) > libfreetype.so.6 => /usr/lib/libfreetype.so.6 (0xb6fb6000) > /lib/ld-linux.so.2 (0xb77e3000) > libk5crypto.so.3 => /usr/lib/libk5crypto.so.3 (0xb6f8d000) > libkrb5support.so.0 => /usr/lib/libkrb5support.so.0 (0xb6f84000) > libkeyutils.so.1 => /lib/libkeyutils.so.1 (0xb6f80000) > libresolv.so.2 => /lib/libresolv.so.2 (0xb6f69000) > liblber-2.4.so.2 => /usr/lib/liblber-2.4.so.2 (0xb6f59000) > libsasl2.so.2 => /usr/lib/libsasl2.so.2 (0xb6f3d000) > libXau.so.6 => /usr/lib/libXau.so.6 (0xb6f39000) > libexpat.so.1 => /lib/libexpat.so.1 (0xb6f0f000) > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > From wo.granon at gmail.com Wed Jan 12 17:48:35 2011 From: wo.granon at gmail.com (wo.granon at gmail.com) Date: Wed, 12 Jan 2011 18:48:35 +0100 Subject: [EMBOSS] error while loading shared libraries: libnucleus.so.6 In-Reply-To: <51851.86.26.12.63.1294853825.squirrel@webmail.ebi.ac.uk> References: <51851.86.26.12.63.1294853825.squirrel@webmail.ebi.ac.uk> Message-ID: Thank you, that did the job! But now i have an other error for which i also can't find anything in the web: # embossversion Error: File /usr/share/EMBOSS/acd/embossversion.acd line 0: ACD file not opened Can you help me again? Thanks, Wolfgang 2011/1/12 : > Hello Wolfgang, > > On OpenSuse that error usually means you've installed EMBOSS into > /usr/local such that the libraries are in /usr/local/lib. That > library directory is cached on OpenSuse so all you should need to do is, > with privilege, type "/sbin/ldconfig" to rebuild the cache. > > HTH > > Alan > > > >> Hello, >> >> I installed stable EMBOSS 6.3.1 on OpenSuse 11.3. >> >> ./configure, make and make install ran without an error. But when I >> try to run an EMBOSS app, i get the following error: >> >> # embossversion >> embossversion: error while loading shared libraries: libnucleus.so.6: >> cannot open shared object file: No such file or directory >> >> I think the attached output could help. Does anyone know what is wrong >> with my installation? Do you need additional data? >> >> Thanks, >> Wolfgang >> >> # ldd $(which embossversion) >> ? ? ? ? linux-gate.so.1 => ?(0xffffe000) >> ? ? ? ? libnucleus.so.6 => not found >> ? ? ? ? libacd.so.6 => not found >> ? ? ? ? libajaxdb.so.6 => not found >> ? ? ? ? libensembl.so.6 => not found >> ? ? ? ? libajaxg.so.6 => not found >> ? ? ? ? libajax.so.6 => not found >> ? ? ? ? libezlib.so.1 => not found >> ? ? ? ? libeexpat.so.1 => not found >> ? ? ? ? libepcre.so.7 => not found >> ? ? ? ? libeplplot.so.3 => not found >> ? ? ? ? libpq.so.5 => /usr/lib/libpq.so.5 (0xb77a4000) >> ? ? ? ? libX11.so.6 => /usr/lib/libX11.so.6 (0xb7669000) >> ? ? ? ? libgd.so.2 => /usr/lib/libgd.so.2 (0xb7622000) >> ? ? ? ? libpng14.so.14 => /usr/lib/libpng14.so.14 (0xb75f6000) >> ? ? ? ? libz.so.1 => /lib/libz.so.1 (0xb75e1000) >> ? ? ? ? libm.so.6 => /lib/libm.so.6 (0xb75b7000) >> ? ? ? ? libc.so.6 => /lib/libc.so.6 (0xb744c000) >> ? ? ? ? libssl.so.1.0.0 => /lib/libssl.so.1.0.0 (0xb73f5000) >> ? ? ? ? libcrypto.so.1.0.0 => /lib/libcrypto.so.1.0.0 (0xb7255000) >> ? ? ? ? libkrb5.so.3 => /usr/lib/libkrb5.so.3 (0xb718d000) >> ? ? ? ? libcom_err.so.2 => /lib/libcom_err.so.2 (0xb7187000) >> ? ? ? ? libgssapi_krb5.so.2 => /usr/lib/libgssapi_krb5.so.2 (0xb7150000) >> ? ? ? ? libldap_r-2.4.so.2 => /usr/lib/libldap_r-2.4.so.2 (0xb7100000) >> ? ? ? ? libpthread.so.0 => /lib/libpthread.so.0 (0xb70e5000) >> ? ? ? ? libxcb.so.1 => /usr/lib/libxcb.so.1 (0xb70c5000) >> ? ? ? ? libdl.so.2 => /lib/libdl.so.2 (0xb70bf000) >> ? ? ? ? libXpm.so.4 => /usr/lib/libXpm.so.4 (0xb70ac000) >> ? ? ? ? libjpeg.so.8 => /usr/lib/libjpeg.so.8 (0xb7073000) >> ? ? ? ? libfontconfig.so.1 => /usr/lib/libfontconfig.so.1 (0xb703d000) >> ? ? ? ? libfreetype.so.6 => /usr/lib/libfreetype.so.6 (0xb6fb6000) >> ? ? ? ? /lib/ld-linux.so.2 (0xb77e3000) >> ? ? ? ? libk5crypto.so.3 => /usr/lib/libk5crypto.so.3 (0xb6f8d000) >> ? ? ? ? libkrb5support.so.0 => /usr/lib/libkrb5support.so.0 (0xb6f84000) >> ? ? ? ? libkeyutils.so.1 => /lib/libkeyutils.so.1 (0xb6f80000) >> ? ? ? ? libresolv.so.2 => /lib/libresolv.so.2 (0xb6f69000) >> ? ? ? ? liblber-2.4.so.2 => /usr/lib/liblber-2.4.so.2 (0xb6f59000) >> ? ? ? ? libsasl2.so.2 => /usr/lib/libsasl2.so.2 (0xb6f3d000) >> ? ? ? ? libXau.so.6 => /usr/lib/libXau.so.6 (0xb6f39000) >> ? ? ? ? libexpat.so.1 => /lib/libexpat.so.1 (0xb6f0f000) >> _______________________________________________ >> EMBOSS mailing list >> EMBOSS at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/emboss >> > > > From wo.granon at gmail.com Wed Jan 12 18:28:42 2011 From: wo.granon at gmail.com (wo.granon at gmail.com) Date: Wed, 12 Jan 2011 19:28:42 +0100 Subject: [EMBOSS] error while loading shared libraries: libnucleus.so.6 In-Reply-To: <45813.86.26.12.63.1294856077.squirrel@webmail.ebi.ac.uk> References: <51851.86.26.12.63.1294853825.squirrel@webmail.ebi.ac.uk> <45813.86.26.12.63.1294856077.squirrel@webmail.ebi.ac.uk> Message-ID: Thank you for your help. Really strange. Following situation: # ls /usr/share/EMBOSS/ emboss.default # ls /usr/local/share/EMBOSS/ acd data doc emboss.default.template jemboss plstnd5.fnt plxtnd5.fnt test Then i looked into /usr/share/EMBOSS/emboss.default, but there is no variable EMBOSS_ACDROOT set. Could it be set elsewhere? Thanks, Wolfgang 2011/1/12 : > Well if you've installed to /usr/local then it should be > looking for that file in /usr/local/share/EMBOSS/acd/embossversion.acd > > As it's looking under /usr/share... my first suspicion would be that > you've set an environment variable incorrectly (e.g. > EMBOSS_ACDROOT). You should not really need to set any EMBOSS > environment variables, it should work OK without. So, if > you have set any such envvars then try unsetting them and run > the program again. > > Alan > > > > >> Thank you, that did the job! But now i have an other error for which i >> also can't find anything in the web: >> >> # embossversion >> Error: File /usr/share/EMBOSS/acd/embossversion.acd line 0: ACD file not >> opened >> >> Can you help me again? >> >> Thanks, >> Wolfgang >> >> 2011/1/12 ?: >>> Hello Wolfgang, >>> >>> On OpenSuse that error usually means you've installed EMBOSS into >>> /usr/local such that the libraries are in /usr/local/lib. That >>> library directory is cached on OpenSuse so all you should need to do is, >>> with privilege, type "/sbin/ldconfig" to rebuild the cache. >>> >>> HTH >>> >>> Alan >>> >>> >>> >>>> Hello, >>>> >>>> I installed stable EMBOSS 6.3.1 on OpenSuse 11.3. >>>> >>>> ./configure, make and make install ran without an error. But when I >>>> try to run an EMBOSS app, i get the following error: >>>> >>>> # embossversion >>>> embossversion: error while loading shared libraries: libnucleus.so.6: >>>> cannot open shared object file: No such file or directory >>>> >>>> I think the attached output could help. Does anyone know what is wrong >>>> with my installation? Do you need additional data? >>>> >>>> Thanks, >>>> Wolfgang >>>> >>>> # ldd $(which embossversion) >>>> ? ? ? ? linux-gate.so.1 => ?(0xffffe000) >>>> ? ? ? ? libnucleus.so.6 => not found >>>> ? ? ? ? libacd.so.6 => not found >>>> ? ? ? ? libajaxdb.so.6 => not found >>>> ? ? ? ? libensembl.so.6 => not found >>>> ? ? ? ? libajaxg.so.6 => not found >>>> ? ? ? ? libajax.so.6 => not found >>>> ? ? ? ? libezlib.so.1 => not found >>>> ? ? ? ? libeexpat.so.1 => not found >>>> ? ? ? ? libepcre.so.7 => not found >>>> ? ? ? ? libeplplot.so.3 => not found >>>> ? ? ? ? libpq.so.5 => /usr/lib/libpq.so.5 (0xb77a4000) >>>> ? ? ? ? libX11.so.6 => /usr/lib/libX11.so.6 (0xb7669000) >>>> ? ? ? ? libgd.so.2 => /usr/lib/libgd.so.2 (0xb7622000) >>>> ? ? ? ? libpng14.so.14 => /usr/lib/libpng14.so.14 (0xb75f6000) >>>> ? ? ? ? libz.so.1 => /lib/libz.so.1 (0xb75e1000) >>>> ? ? ? ? libm.so.6 => /lib/libm.so.6 (0xb75b7000) >>>> ? ? ? ? libc.so.6 => /lib/libc.so.6 (0xb744c000) >>>> ? ? ? ? libssl.so.1.0.0 => /lib/libssl.so.1.0.0 (0xb73f5000) >>>> ? ? ? ? libcrypto.so.1.0.0 => /lib/libcrypto.so.1.0.0 (0xb7255000) >>>> ? ? ? ? libkrb5.so.3 => /usr/lib/libkrb5.so.3 (0xb718d000) >>>> ? ? ? ? libcom_err.so.2 => /lib/libcom_err.so.2 (0xb7187000) >>>> ? ? ? ? libgssapi_krb5.so.2 => /usr/lib/libgssapi_krb5.so.2 >>>> (0xb7150000) >>>> ? ? ? ? libldap_r-2.4.so.2 => /usr/lib/libldap_r-2.4.so.2 (0xb7100000) >>>> ? ? ? ? libpthread.so.0 => /lib/libpthread.so.0 (0xb70e5000) >>>> ? ? ? ? libxcb.so.1 => /usr/lib/libxcb.so.1 (0xb70c5000) >>>> ? ? ? ? libdl.so.2 => /lib/libdl.so.2 (0xb70bf000) >>>> ? ? ? ? libXpm.so.4 => /usr/lib/libXpm.so.4 (0xb70ac000) >>>> ? ? ? ? libjpeg.so.8 => /usr/lib/libjpeg.so.8 (0xb7073000) >>>> ? ? ? ? libfontconfig.so.1 => /usr/lib/libfontconfig.so.1 (0xb703d000) >>>> ? ? ? ? libfreetype.so.6 => /usr/lib/libfreetype.so.6 (0xb6fb6000) >>>> ? ? ? ? /lib/ld-linux.so.2 (0xb77e3000) >>>> ? ? ? ? libk5crypto.so.3 => /usr/lib/libk5crypto.so.3 (0xb6f8d000) >>>> ? ? ? ? libkrb5support.so.0 => /usr/lib/libkrb5support.so.0 >>>> (0xb6f84000) >>>> ? ? ? ? libkeyutils.so.1 => /lib/libkeyutils.so.1 (0xb6f80000) >>>> ? ? ? ? libresolv.so.2 => /lib/libresolv.so.2 (0xb6f69000) >>>> ? ? ? ? liblber-2.4.so.2 => /usr/lib/liblber-2.4.so.2 (0xb6f59000) >>>> ? ? ? ? libsasl2.so.2 => /usr/lib/libsasl2.so.2 (0xb6f3d000) >>>> ? ? ? ? libXau.so.6 => /usr/lib/libXau.so.6 (0xb6f39000) >>>> ? ? ? ? libexpat.so.1 => /lib/libexpat.so.1 (0xb6f0f000) >>>> _______________________________________________ >>>> EMBOSS mailing list >>>> EMBOSS at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/emboss >>>> >>> >>> >>> >> > > > From wo.granon at gmail.com Wed Jan 12 18:41:47 2011 From: wo.granon at gmail.com (wo.granon at gmail.com) Date: Wed, 12 Jan 2011 19:41:47 +0100 Subject: [EMBOSS] error while loading shared libraries: libnucleus.so.6 In-Reply-To: References: <51851.86.26.12.63.1294853825.squirrel@webmail.ebi.ac.uk> <45813.86.26.12.63.1294856077.squirrel@webmail.ebi.ac.uk> Message-ID: Thank you, problem solved. Starting the system new solved the problem ;-) There must have been some variables from a previous installation set. Wolfgang 2011/1/12 : > Thank you for your help. Really strange. > > Following situation: > # ls ?/usr/share/EMBOSS/ > emboss.default > # ls /usr/local/share/EMBOSS/ > acd ?data ?doc ?emboss.default.template ?jemboss ?plstnd5.fnt ?plxtnd5.fnt ?test > > Then i looked into /usr/share/EMBOSS/emboss.default, but there is no > variable EMBOSS_ACDROOT set. Could it be set elsewhere? > > Thanks, > Wolfgang > > > > > > 2011/1/12 ?: >> Well if you've installed to /usr/local then it should be >> looking for that file in /usr/local/share/EMBOSS/acd/embossversion.acd >> >> As it's looking under /usr/share... my first suspicion would be that >> you've set an environment variable incorrectly (e.g. >> EMBOSS_ACDROOT). You should not really need to set any EMBOSS >> environment variables, it should work OK without. So, if >> you have set any such envvars then try unsetting them and run >> the program again. >> >> Alan >> >> >> >> >>> Thank you, that did the job! But now i have an other error for which i >>> also can't find anything in the web: >>> >>> # embossversion >>> Error: File /usr/share/EMBOSS/acd/embossversion.acd line 0: ACD file not >>> opened >>> >>> Can you help me again? >>> >>> Thanks, >>> Wolfgang >>> >>> 2011/1/12 ?: >>>> Hello Wolfgang, >>>> >>>> On OpenSuse that error usually means you've installed EMBOSS into >>>> /usr/local such that the libraries are in /usr/local/lib. That >>>> library directory is cached on OpenSuse so all you should need to do is, >>>> with privilege, type "/sbin/ldconfig" to rebuild the cache. >>>> >>>> HTH >>>> >>>> Alan >>>> >>>> >>>> >>>>> Hello, >>>>> >>>>> I installed stable EMBOSS 6.3.1 on OpenSuse 11.3. >>>>> >>>>> ./configure, make and make install ran without an error. But when I >>>>> try to run an EMBOSS app, i get the following error: >>>>> >>>>> # embossversion >>>>> embossversion: error while loading shared libraries: libnucleus.so.6: >>>>> cannot open shared object file: No such file or directory >>>>> >>>>> I think the attached output could help. Does anyone know what is wrong >>>>> with my installation? Do you need additional data? >>>>> >>>>> Thanks, >>>>> Wolfgang >>>>> >>>>> # ldd $(which embossversion) >>>>> ? ? ? ? linux-gate.so.1 => ?(0xffffe000) >>>>> ? ? ? ? libnucleus.so.6 => not found >>>>> ? ? ? ? libacd.so.6 => not found >>>>> ? ? ? ? libajaxdb.so.6 => not found >>>>> ? ? ? ? libensembl.so.6 => not found >>>>> ? ? ? ? libajaxg.so.6 => not found >>>>> ? ? ? ? libajax.so.6 => not found >>>>> ? ? ? ? libezlib.so.1 => not found >>>>> ? ? ? ? libeexpat.so.1 => not found >>>>> ? ? ? ? libepcre.so.7 => not found >>>>> ? ? ? ? libeplplot.so.3 => not found >>>>> ? ? ? ? libpq.so.5 => /usr/lib/libpq.so.5 (0xb77a4000) >>>>> ? ? ? ? libX11.so.6 => /usr/lib/libX11.so.6 (0xb7669000) >>>>> ? ? ? ? libgd.so.2 => /usr/lib/libgd.so.2 (0xb7622000) >>>>> ? ? ? ? libpng14.so.14 => /usr/lib/libpng14.so.14 (0xb75f6000) >>>>> ? ? ? ? libz.so.1 => /lib/libz.so.1 (0xb75e1000) >>>>> ? ? ? ? libm.so.6 => /lib/libm.so.6 (0xb75b7000) >>>>> ? ? ? ? libc.so.6 => /lib/libc.so.6 (0xb744c000) >>>>> ? ? ? ? libssl.so.1.0.0 => /lib/libssl.so.1.0.0 (0xb73f5000) >>>>> ? ? ? ? libcrypto.so.1.0.0 => /lib/libcrypto.so.1.0.0 (0xb7255000) >>>>> ? ? ? ? libkrb5.so.3 => /usr/lib/libkrb5.so.3 (0xb718d000) >>>>> ? ? ? ? libcom_err.so.2 => /lib/libcom_err.so.2 (0xb7187000) >>>>> ? ? ? ? libgssapi_krb5.so.2 => /usr/lib/libgssapi_krb5.so.2 >>>>> (0xb7150000) >>>>> ? ? ? ? libldap_r-2.4.so.2 => /usr/lib/libldap_r-2.4.so.2 (0xb7100000) >>>>> ? ? ? ? libpthread.so.0 => /lib/libpthread.so.0 (0xb70e5000) >>>>> ? ? ? ? libxcb.so.1 => /usr/lib/libxcb.so.1 (0xb70c5000) >>>>> ? ? ? ? libdl.so.2 => /lib/libdl.so.2 (0xb70bf000) >>>>> ? ? ? ? libXpm.so.4 => /usr/lib/libXpm.so.4 (0xb70ac000) >>>>> ? ? ? ? libjpeg.so.8 => /usr/lib/libjpeg.so.8 (0xb7073000) >>>>> ? ? ? ? libfontconfig.so.1 => /usr/lib/libfontconfig.so.1 (0xb703d000) >>>>> ? ? ? ? libfreetype.so.6 => /usr/lib/libfreetype.so.6 (0xb6fb6000) >>>>> ? ? ? ? /lib/ld-linux.so.2 (0xb77e3000) >>>>> ? ? ? ? libk5crypto.so.3 => /usr/lib/libk5crypto.so.3 (0xb6f8d000) >>>>> ? ? ? ? libkrb5support.so.0 => /usr/lib/libkrb5support.so.0 >>>>> (0xb6f84000) >>>>> ? ? ? ? libkeyutils.so.1 => /lib/libkeyutils.so.1 (0xb6f80000) >>>>> ? ? ? ? libresolv.so.2 => /lib/libresolv.so.2 (0xb6f69000) >>>>> ? ? ? ? liblber-2.4.so.2 => /usr/lib/liblber-2.4.so.2 (0xb6f59000) >>>>> ? ? ? ? libsasl2.so.2 => /usr/lib/libsasl2.so.2 (0xb6f3d000) >>>>> ? ? ? ? libXau.so.6 => /usr/lib/libXau.so.6 (0xb6f39000) >>>>> ? ? ? ? libexpat.so.1 => /lib/libexpat.so.1 (0xb6f0f000) >>>>> _______________________________________________ >>>>> EMBOSS mailing list >>>>> EMBOSS at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/emboss >>>>> >>>> >>>> >>>> >>> >> >> >> > From wo.granon at gmail.com Sun Jan 16 11:45:57 2011 From: wo.granon at gmail.com (wo.granon at gmail.com) Date: Sun, 16 Jan 2011 12:45:57 +0100 Subject: [EMBOSS] cirdna and Text inside or outside of blocks In-Reply-To: References: Message-ID: Hello, I have following problem with cirdna an Text inside or outside of blocks: If I use the example input file from the manual: http://emboss.sourceforge.net/apps/release/6.3/emboss/apps/cirdna.html#input.1 and "-posblocks 1" the given block text ist _not_ printed. If I use "-posblocks 2" the text is printed, but in a not readable way: http://tinypic.com/r/20t5wzs/7 Can you tell me what I do wrong or if this is a bug? Thanks, Wolfgang From wo.granon at gmail.com Sun Jan 16 12:56:07 2011 From: wo.granon at gmail.com (wo.granon at gmail.com) Date: Sun, 16 Jan 2011 13:56:07 +0100 Subject: [EMBOSS] cirdna and Text inside or outside of blocks In-Reply-To: References: Message-ID: Here a little bigger: http://tinypic.com/r/2010x8n/7 It looks like that there is no space between the characters. Thanks, Wolfgang 2011/1/16 : > Hello, > > I have following problem with cirdna an Text inside or outside of blocks: > > If I use the example input file from the manual: > http://emboss.sourceforge.net/apps/release/6.3/emboss/apps/cirdna.html#input.1 > > and "-posblocks 1" the given block text ist _not_ printed. If I use > "-posblocks 2" the text is printed, but in a not readable way: > http://tinypic.com/r/20t5wzs/7 > > Can you tell me what I do wrong or if this is a bug? > > Thanks, > Wolfgang > From stephen.taylor at imm.ox.ac.uk Wed Jan 19 16:09:01 2011 From: stephen.taylor at imm.ox.ac.uk (Stephen Taylor) Date: Wed, 19 Jan 2011 16:09:01 +0000 Subject: [EMBOSS] SAM format Message-ID: <4D370C9D.5080902@imm.ox.ac.uk> Hi, Is EMBOSS planning to release tools that produce SAM format in the near future or is it more likely to be on the customary July 15th release? Kind regards and thanks, Steve From pmr at ebi.ac.uk Thu Jan 20 08:16:39 2011 From: pmr at ebi.ac.uk (Peter Rice) Date: Thu, 20 Jan 2011 08:16:39 +0000 Subject: [EMBOSS] SAM format In-Reply-To: <4D370C9D.5080902@imm.ox.ac.uk> References: <4D370C9D.5080902@imm.ox.ac.uk> Message-ID: <4D37EF67.1080206@ebi.ac.uk> On 01/19/11 16:09, Stephen Taylor wrote: > Hi, > > Is EMBOSS planning to release tools that produce SAM format in the near > future or is it more likely to be on the customary July 15th release? The last release EMBOSS 6.3.1 has SAM as an output format for sequences and pairwise alignments (-oformat sam and -aformat sam respectively). What data would you like to represent in SAM format, and are there extra fields you would like us to include? regards, Peter Rice From stephen.taylor at imm.ox.ac.uk Thu Jan 20 09:06:59 2011 From: stephen.taylor at imm.ox.ac.uk (Stephen Taylor) Date: Thu, 20 Jan 2011 09:06:59 +0000 Subject: [EMBOSS] SAM format In-Reply-To: <4D37EF67.1080206@ebi.ac.uk> References: <4D370C9D.5080902@imm.ox.ac.uk> <4D37EF67.1080206@ebi.ac.uk> Message-ID: <4D37FB33.8060801@imm.ox.ac.uk> Hi Peter, >> >> Is EMBOSS planning to release tools that produce SAM format in the near >> future or is it more likely to be on the customary July 15th release? > > The last release EMBOSS 6.3.1 has SAM as an output format for sequences > and pairwise alignments (-oformat sam and -aformat sam respectively). > > What data would you like to represent in SAM format, and are there extra > fields you would like us to include? > So it does! Excellent. Sadly, fuzznuc doesn't seem to work using aformat or oformat. Is that due to be supported? Thanks, Steve From pmr at ebi.ac.uk Thu Jan 20 09:36:00 2011 From: pmr at ebi.ac.uk (Peter Rice) Date: Thu, 20 Jan 2011 09:36:00 +0000 Subject: [EMBOSS] SAM format In-Reply-To: <4D37FB33.8060801@imm.ox.ac.uk> References: <4D370C9D.5080902@imm.ox.ac.uk> <4D37EF67.1080206@ebi.ac.uk> <4D37FB33.8060801@imm.ox.ac.uk> Message-ID: <4D380200.7080806@ebi.ac.uk> On 01/20/11 09:06, Stephen Taylor wrote: > Hi Peter, > >>> >>> Is EMBOSS planning to release tools that produce SAM format in the near >>> future or is it more likely to be on the customary July 15th release? >> >> The last release EMBOSS 6.3.1 has SAM as an output format for sequences >> and pairwise alignments (-oformat sam and -aformat sam respectively). ... oops, -osformat for sequences of course. > Sadly, fuzznuc doesn't seem to work using aformat or oformat. Is that > due to be supported? Ah, fuzznuc reports features so we hadn't implemented SAM there. However, you can use -rformat listfile to get USAs for the features, and then seqret -osformat sam @listfilename to get the sequences in SAM format. Possibly scope to do more there. What would you like to see in SAM output for fuzznuc? regards, Peter From pmr at ebi.ac.uk Thu Jan 20 09:40:35 2011 From: pmr at ebi.ac.uk (Peter Rice) Date: Thu, 20 Jan 2011 09:40:35 +0000 Subject: [EMBOSS] SAM format In-Reply-To: <4D37FDB9.7000804@imm.ox.ac.uk> References: <4D370C9D.5080902@imm.ox.ac.uk> <4D37EF67.1080206@ebi.ac.uk> <4D37FDB9.7000804@imm.ox.ac.uk> Message-ID: <4D380313.7030106@ebi.ac.uk> On 01/20/11 09:17, Stephen Taylor wrote: > Is there a bug in the gff3 output of fuzznuc? > > ##gff-version 3 > ##sequence-region chr21 1 46944323 > #!Date 2011-01-20 > #!Type DNA > #!Source-version EMBOSS 6.3.1 > chr21 fuzznuc nucleotide_motif 13362906 13362942 37.000 + . ID="chr21.1";note="*pat pattern" > > It would be nice to actually show the pattern matched in the note field. or both. What it shows is the "name" of the pattern, which usually defaults to pattern. We could show the name and then the pattern. I will add it to the next release. Thanks for the suggestion. Peter From stephen.taylor at imm.ox.ac.uk Thu Jan 20 09:17:45 2011 From: stephen.taylor at imm.ox.ac.uk (Stephen Taylor) Date: Thu, 20 Jan 2011 09:17:45 +0000 Subject: [EMBOSS] SAM format In-Reply-To: <4D37EF67.1080206@ebi.ac.uk> References: <4D370C9D.5080902@imm.ox.ac.uk> <4D37EF67.1080206@ebi.ac.uk> Message-ID: <4D37FDB9.7000804@imm.ox.ac.uk> On 20/01/2011 08:16, Peter Rice wrote: > On 01/19/11 16:09, Stephen Taylor wrote: >> Hi, >> >> Is EMBOSS planning to release tools that produce SAM format in the near >> future or is it more likely to be on the customary July 15th release? > > The last release EMBOSS 6.3.1 has SAM as an output format for sequences > and pairwise alignments (-oformat sam and -aformat sam respectively). > > What data would you like to represent in SAM format, and are there extra > fields you would like us to include? Also... Is there a bug in the gff3 output of fuzznuc? ##gff-version 3 ##sequence-region chr21 1 46944323 #!Date 2011-01-20 #!Type DNA #!Source-version EMBOSS 6.3.1 chr21 fuzznuc nucleotide_motif 13362906 13362942 37.000 + . ID="chr21.1";note="*pat pattern" It would be nice to actually show the pattern matched in the note field. Thanks, Steve From stephen.taylor at imm.ox.ac.uk Thu Jan 20 10:36:20 2011 From: stephen.taylor at imm.ox.ac.uk (Stephen Taylor) Date: Thu, 20 Jan 2011 10:36:20 +0000 Subject: [EMBOSS] SAM format In-Reply-To: <4D380200.7080806@ebi.ac.uk> References: <4D370C9D.5080902@imm.ox.ac.uk> <4D37EF67.1080206@ebi.ac.uk> <4D37FB33.8060801@imm.ox.ac.uk> <4D380200.7080806@ebi.ac.uk> Message-ID: <4D381024.1010001@imm.ox.ac.uk> On 20/01/2011 09:36, Peter Rice wrote: > On 01/20/11 09:06, Stephen Taylor wrote: >> Hi Peter, >> >>>> >>>> Is EMBOSS planning to release tools that produce SAM format in the near >>>> future or is it more likely to be on the customary July 15th release? >>> >>> The last release EMBOSS 6.3.1 has SAM as an output format for sequences >>> and pairwise alignments (-oformat sam and -aformat sam respectively). > > ... oops, -osformat for sequences of course. > > >> Sadly, fuzznuc doesn't seem to work using aformat or oformat. Is that >> due to be supported? > > Ah, fuzznuc reports features so we hadn't implemented SAM there. > > However, you can use -rformat listfile to get USAs for the features, and > then seqret -osformat sam @listfilename to get the sequences in SAM format. > > Possibly scope to do more there. What would you like to see in SAM > output for fuzznuc? My motivation was to build BAM tracks showing matches of lots of patterns in the genome sequence. I hadn't thought about proteins but I guess you could so something similar. The SAM file would show the position of each match per line and the CIGAR string containing the matched pattern and SEQ (col 10) containing the query pattern expanded to show the match. The original pattern could be in the OPT field. I see there is a tag for Mismatching positions (MD) which would work for regex style matches (so good for 'dreg'), but I am not sure it would be strictly legal for a PROSITE like pattern. e.g for [CG](5)TG{A}N(1,5)C Could you have MD:Z:[CG](5)TG{A}N(1,5)C ? It looks like {,} is not allowed. So perhaps you would have to translate the pattern to a regex or generate an alternative optional tag. I am not a SAM expert so apologies if I am proposing to violate the format rules! Incidentally, I would use dreg but it doesn't allow mismatches to be easily specified. Steve From pmr at ebi.ac.uk Thu Jan 20 10:54:33 2011 From: pmr at ebi.ac.uk (Peter Rice) Date: Thu, 20 Jan 2011 10:54:33 +0000 Subject: [EMBOSS] SAM format In-Reply-To: <4D381024.1010001@imm.ox.ac.uk> References: <4D370C9D.5080902@imm.ox.ac.uk> <4D37EF67.1080206@ebi.ac.uk> <4D37FB33.8060801@imm.ox.ac.uk> <4D380200.7080806@ebi.ac.uk> <4D381024.1010001@imm.ox.ac.uk> Message-ID: <4D381469.2020503@ebi.ac.uk> On 01/20/11 10:36, Stephen Taylor wrote: > On 20/01/2011 09:36, Peter Rice wrote: >> Possibly scope to do more there. What would you like to see in SAM >> output for fuzznuc? > > My motivation was to build BAM tracks showing matches of lots of > patterns in the genome sequence. I hadn't thought about proteins but I > guess you could so something similar. > > The SAM file would show the position of each match per line and the > CIGAR string containing the matched pattern and SEQ (col 10) containing > the query pattern expanded to show the match. The original pattern could > be in the OPT field. Interesting. The sequence becomes the reference. We would have to do a little extra work to generate the CIGAR string for various patterns but that should be possible but modifying the pattern matching code. >I see there is a tag for Mismatching positions (MD) > which would work for regex style matches (so good for 'dreg'), but I am > not sure it would be strictly legal for a PROSITE like pattern. > > e.g for [CG](5)TG{A}N(1,5)C > > Could you have > > MD:Z:[CG](5)TG{A}N(1,5)C That will need some investigation. Maybe prosite patterns can be translated to regex for this purpose - many will convert easily. > It looks like {,} is not allowed. So perhaps you would have to translate > the pattern to a regex or generate an alternative optional tag. I am not > a SAM expert so apologies if I am proposing to violate the format rules! N(1,5) is equivalent to NN?N?N?N? ... though prosite ranges can go over 100 positions. > Incidentally, I would use dreg but it doesn't allow mismatches to be > easily specified. True, that's a regular expression library issue. regards, Peter From stephen.taylor at imm.ox.ac.uk Mon Jan 24 11:09:05 2011 From: stephen.taylor at imm.ox.ac.uk (Stephen Taylor) Date: Mon, 24 Jan 2011 11:09:05 +0000 Subject: [EMBOSS] SAM format In-Reply-To: <4D380313.7030106@ebi.ac.uk> References: <4D370C9D.5080902@imm.ox.ac.uk> <4D37EF67.1080206@ebi.ac.uk> <4D37FDB9.7000804@imm.ox.ac.uk> <4D380313.7030106@ebi.ac.uk> Message-ID: <4D3D5DD1.8090303@imm.ox.ac.uk> Hi again Peter, > On 01/20/11 09:17, Stephen Taylor wrote: > >> Is there a bug in the gff3 output of fuzznuc? >> >> ##gff-version 3 >> ##sequence-region chr21 1 46944323 >> #!Date 2011-01-20 >> #!Type DNA >> #!Source-version EMBOSS 6.3.1 >> chr21 fuzznuc nucleotide_motif 13362906 13362942 37.000 + . ID="chr21.1";note="*pat pattern" >> >> It would be nice to actually show the pattern matched in the note field. > > or both. What it shows is the "name" of the pattern, which usually > defaults to pattern. Please can you define 'usually' i.e. What are the 'rules' for getting it to show the pattern? Usual behaviour when I run it, is it shows note="*pat pattern". Thanks, Steve From pmr at ebi.ac.uk Mon Jan 24 11:45:39 2011 From: pmr at ebi.ac.uk (Peter Rice) Date: Mon, 24 Jan 2011 11:45:39 +0000 Subject: [EMBOSS] SAM format In-Reply-To: <4D3D5DD1.8090303@imm.ox.ac.uk> References: <4D370C9D.5080902@imm.ox.ac.uk> <4D37EF67.1080206@ebi.ac.uk> <4D37FDB9.7000804@imm.ox.ac.uk> <4D380313.7030106@ebi.ac.uk> <4D3D5DD1.8090303@imm.ox.ac.uk> Message-ID: <4D3D6663.1090402@ebi.ac.uk> On 24/01/11 11:09, Stephen Taylor wrote: > Hi again Peter, > >> On 01/20/11 09:17, Stephen Taylor wrote: >> >>> Is there a bug in the gff3 output of fuzznuc? >>> >>> ##gff-version 3 >>> ##sequence-region chr21 1 46944323 >>> #!Date 2011-01-20 >>> #!Type DNA >>> #!Source-version EMBOSS 6.3.1 >>> chr21 fuzznuc nucleotide_motif 13362906 13362942 37.000 + . >>> ID="chr21.1";note="*pat pattern" >>> >>> It would be nice to actually show the pattern matched in the note field. >> >> or both. What it shows is the "name" of the pattern, which usually >> defaults to pattern. > > Please can you define 'usually' i.e. What are the 'rules' for getting it > to show the pattern? Usual behaviour when I run it, is it shows > note="*pat pattern". The pattern name defaults to 'pattern'. This will always be the case when the user specifies a pattern on the command line with no other options. Where multiple patterns are defined in an input file ('filename syntax for the pattern), each has a unique name in the file. The pattern name can also be set via the -pname qualifier. So it makes sense to include the pattern string in the qualifier value, and to rename it to "Pattern" in the report output. regards, Peter From stephen.taylor at imm.ox.ac.uk Mon Jan 24 11:56:52 2011 From: stephen.taylor at imm.ox.ac.uk (Stephen Taylor) Date: Mon, 24 Jan 2011 11:56:52 +0000 Subject: [EMBOSS] SAM format In-Reply-To: <4D3D6663.1090402@ebi.ac.uk> References: <4D370C9D.5080902@imm.ox.ac.uk> <4D37EF67.1080206@ebi.ac.uk> <4D37FDB9.7000804@imm.ox.ac.uk> <4D380313.7030106@ebi.ac.uk> <4D3D5DD1.8090303@imm.ox.ac.uk> <4D3D6663.1090402@ebi.ac.uk> Message-ID: <4D3D6904.6050604@imm.ox.ac.uk> On 24/01/2011 11:45, Peter Rice wrote: > On 24/01/11 11:09, Stephen Taylor wrote: >> Hi again Peter, >> >>> On 01/20/11 09:17, Stephen Taylor wrote: >>> >>>> Is there a bug in the gff3 output of fuzznuc? >>>> >>>> ##gff-version 3 >>>> ##sequence-region chr21 1 46944323 >>>> #!Date 2011-01-20 >>>> #!Type DNA >>>> #!Source-version EMBOSS 6.3.1 >>>> chr21 fuzznuc nucleotide_motif 13362906 13362942 37.000 + . >>>> ID="chr21.1";note="*pat pattern" >>>> >>>> It would be nice to actually show the pattern matched in the note field. >>> >>> or both. What it shows is the "name" of the pattern, which usually >>> defaults to pattern. >> >> Please can you define 'usually' i.e. What are the 'rules' for getting it >> to show the pattern? Usual behaviour when I run it, is it shows >> note="*pat pattern". > > The pattern name defaults to 'pattern'. This will always be the case > when the user specifies a pattern on the command line with no other options. > > Where multiple patterns are defined in an input file ('filename syntax > for the pattern), each has a unique name in the file. > > The pattern name can also be set via the -pname qualifier. > > So it makes sense to include the pattern string in the qualifier value, > and to rename it to "Pattern" in the report output. > I see. Many thanks for clearing that up. Steve From stephen.taylor at imm.ox.ac.uk Tue Jan 25 10:03:14 2011 From: stephen.taylor at imm.ox.ac.uk (Stephen Taylor) Date: Tue, 25 Jan 2011 10:03:14 +0000 Subject: [EMBOSS] GFF no header Message-ID: <4D3E9FE2.4090008@imm.ox.ac.uk> Hi, I seem to remember there was an option in EMBOSS that returned a GFF3 report format without its '#' header. Please can somebody remind me what it is? Thanks a lot, Steve From wo.granon at gmail.com Wed Jan 26 08:13:27 2011 From: wo.granon at gmail.com (Wolfgang Gruber) Date: Wed, 26 Jan 2011 09:13:27 +0100 Subject: [EMBOSS] Retrieve data from entrez Message-ID: Hello, i am not sure if I did it the right way. I wanted to access the entrez database, because in general I get my sequences from there. I putted this entry into my emboss.default: DB entrez [ type: N format: genbank method: entrez fields: "id acc gi sv des org key" url: "http://www.ncbi.nlm.nih.gov/sites/gquery" ] Then i tried to retrieve the data with the entrez id. In most cases this works, in some not. For example seqret entrez:NM_000527 works, but seqret entrez:NP_000518 does not: "Error: Unable to read sequence 'entrez:NP_000518'" Can you help me what I did wrong? Ones more what I want: I want to give the entrez id and retrieve then the corresponding sequence. Thanks, Wolfgang From david.bauer at bayer.com Wed Jan 26 08:39:28 2011 From: david.bauer at bayer.com (david.bauer at bayer.com) Date: Wed, 26 Jan 2011 09:39:28 +0100 Subject: [EMBOSS] Antwort: Retrieve data from entrez In-Reply-To: Message-ID: Hi, the entrez method looks at the type (N or P) to formulate the eutils request to the ncbi server. As NP_ is a protein sequence, the database specified in the request must be protein and not nucleotide. So you need two separate entries in emboss.default for nucleotide and protein sequences. David. emboss-bounces at lists.open-bio.org schrieb am 26/01/2011 09:13:27: > Hello, > > i am not sure if I did it the right way. I wanted to access the entrez > database, because in general I get my sequences from there. I putted > this entry into my emboss.default: > > DB entrez [ > type: N > format: genbank > method: entrez > fields: "id acc gi sv des org key" > url: "http://www.ncbi.nlm.nih.gov/sites/gquery" > ] > > Then i tried to retrieve the data with the entrez id. In most cases > this works, in some not. For example seqret entrez:NM_000527 works, > but seqret entrez:NP_000518 does not: "Error: Unable to read sequence > 'entrez:NP_000518'" > > Can you help me what I did wrong? > > Ones more what I want: I want to give the entrez id and retrieve then > the corresponding sequence. > > Thanks, > Wolfgang > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss From hrh at fmi.ch Wed Jan 26 08:49:42 2011 From: hrh at fmi.ch (Hans-Rudolf Hotz) Date: Wed, 26 Jan 2011 09:49:42 +0100 Subject: [EMBOSS] Retrieve data from entrez In-Reply-To: References: Message-ID: <4D3FE026.4010502@fmi.ch> Hi Wolfgang 'NP_000518' is a protein entry. You can fetch it by adding a second database definition (with "type: P"), ie: DB entrezP [ type: P format: genbank method: entrez fields: "id acc gi sv des org key" url: "http://www.ncbi.nlm.nih.gov/sites/gquery" ] and then you can fetch the protein sequence: -bash-3.2$ seqret entrezP:NP_000518 -auto stdout |head -3 >NP_000518 NP_000518.1 low-density lipoprotein receptor isoform 1 precursor [Homo sapiens]. mgpwgwklrwtvalllaaagtavgdrcernefqcqdgkcisykwvcdgsaecqdgsdesq etclsvtcksgdfscggrvnrcipqfwrcdgqvdcdngsdeqgcppktcsqdefrchdgk -bash-3.2$ Regards, Hans On 01/26/2011 09:13 AM, Wolfgang Gruber wrote: > Hello, > > i am not sure if I did it the right way. I wanted to access the entrez > database, because in general I get my sequences from there. I putted > this entry into my emboss.default: > > DB entrez [ > type: N > format: genbank > method: entrez > fields: "id acc gi sv des org key" > url: "http://www.ncbi.nlm.nih.gov/sites/gquery" > ] > > Then i tried to retrieve the data with the entrez id. In most cases > this works, in some not. For example seqret entrez:NM_000527 works, > but seqret entrez:NP_000518 does not: "Error: Unable to read sequence > 'entrez:NP_000518'" > > Can you help me what I did wrong? > > Ones more what I want: I want to give the entrez id and retrieve then > the corresponding sequence. > > Thanks, > Wolfgang > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss From wo.granon at gmail.com Wed Jan 26 09:47:31 2011 From: wo.granon at gmail.com (Wolfgang Gruber) Date: Wed, 26 Jan 2011 10:47:31 +0100 Subject: [EMBOSS] Retrieve data from entrez In-Reply-To: <4D3FE026.4010502@fmi.ch> References: <4D3FE026.4010502@fmi.ch> Message-ID: I understand. Thank you very much! I didn't recognize the type switch. In general: Is this way ok to get the Sequences behind an entrez id? Or is there a more specific way? Because this way I can also specify a search term and then I get more than one result. Thanks, Wolfgang 2011/1/26 Hans-Rudolf Hotz : > Hi Wolfgang > > 'NP_000518' is a protein entry. You can fetch it by adding a second database > definition (with "type: P"), ie: > > > DB entrezP [ > ? ? ? ? type: P > ? ? ? ? format: genbank > ? ? ? ? method: entrez > ? ? ? ? fields: "id acc gi sv des org key" > ? ? ? ? url: ? ?"http://www.ncbi.nlm.nih.gov/sites/gquery" > ] > > > and then you can fetch the protein sequence: > > > -bash-3.2$ seqret entrezP:NP_000518 -auto stdout |head -3 >>NP_000518 NP_000518.1 low-density lipoprotein receptor isoform 1 precursor >> [Homo sapiens]. > mgpwgwklrwtvalllaaagtavgdrcernefqcqdgkcisykwvcdgsaecqdgsdesq > etclsvtcksgdfscggrvnrcipqfwrcdgqvdcdngsdeqgcppktcsqdefrchdgk > -bash-3.2$ > > > Regards, Hans > > > > On 01/26/2011 09:13 AM, Wolfgang Gruber wrote: >> >> Hello, >> >> i am not sure if I did it the right way. I wanted to access the entrez >> database, because in general I get my sequences from there. I putted >> this entry into my emboss.default: >> >> DB entrez [ >> ? ? ? ? ?type: N >> ? ? ? ? ?format: genbank >> ? ? ? ? ?method: entrez >> ? ? ? ? ?fields: "id acc gi sv des org key" >> ? ? ? ? ?url: ? ?"http://www.ncbi.nlm.nih.gov/sites/gquery" >> ] >> >> Then i tried to retrieve the data with the entrez id. In most cases >> this works, in some not. For example seqret entrez:NM_000527 works, >> but seqret entrez:NP_000518 does not: "Error: Unable to read sequence >> 'entrez:NP_000518'" >> >> Can you help me what I did wrong? >> >> Ones more what I want: I want to give the entrez id and retrieve then >> the corresponding sequence. >> >> Thanks, >> Wolfgang >> _______________________________________________ >> EMBOSS mailing list >> EMBOSS at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/emboss > From Lionel.Brooks at dartmouth.edu Thu Jan 27 23:02:42 2011 From: Lionel.Brooks at dartmouth.edu (Lionel (Lee) Brooks 3rd) Date: Thu, 27 Jan 2011 18:02:42 -0500 Subject: [EMBOSS] dreg: does it search both strands? Message-ID: <4D41F992.5030900@dartmouth.edu> Hello fellow EMBOSS fans, I am using the dreg program to search the human genome for my favorite motif. I was unable to find any information regarding the meaning of the strand information in the output. Does dreg search both strands or will it always return "+" as the strand designation of the hits that it finds? Thanks for your continued support and development of this fantastic tool! Sincerely, Lionel "Lee" Brooks 3rd Dartmouth Genetics Grad Student From robin at hms.harvard.edu Fri Jan 28 19:51:27 2011 From: robin at hms.harvard.edu (Robin Colgrove) Date: Fri, 28 Jan 2011 14:51:27 -0500 Subject: [EMBOSS] Batch alignments? In-Reply-To: <4D41F992.5030900@dartmouth.edu> References: <4D41F992.5030900@dartmouth.edu> Message-ID: Hello EMBOSS-folk. Given a set of fasta files, each an ordered list of coding sequences for a set of highly homologous (viral) genomes, is there some straightforward way of generating a file with alignments of the coding sequences other than doing each one manually (around a 100 genes). That is, if each file is of the form: >gene1 ATG... ...TAG >gene2 ATG... ...TAA etc.... I want to align each set of homologous genes. I've used matcher and needle to do a gene at a time, but it would be nice to batch this. thanks, Robin Colgrove Harvard Medical School PS: Embarrassingly enough, I am using v3.0.0 of emboss (Mac OS X 10.6.5). Can I just install a new version or do I have to uninstall everything first? Looking for the minimum fuss route. From db60 at st-andrews.ac.uk Sat Jan 29 12:08:34 2011 From: db60 at st-andrews.ac.uk (Daniel Barker) Date: Sat, 29 Jan 2011 12:08:34 +0000 Subject: [EMBOSS] Batch alignments? In-Reply-To: References: <4D41F992.5030900@dartmouth.edu> Message-ID: <4D440342.8060703@st-andrews.ac.uk> Dear Robin, In a Perl script, you could read your sequences using BioPerl Seq::IO, create input files, and execute the EMBOSS commands from Perl with system() or `...`. Remember to close temporary files you've created in Perl before using them - this forces the last bit of the file to be really written, rather than stay languishing in some buffer. This is just one suggestion - there will be other ways. An excellent guide to Perl is at: http://korflab.ucdavis.edu/Unix_and_Perl If I remember, some earlier version of needle had a bug which could affect scores. So you might want to upgrade. For coding sequences, consider doing the alignment at the protein level - unless there's a good reason not to. I.e. translate your coding sequences (perhaps with EMBOSS transeq) and align the translations. Generally, this will be more sensitive and less easily misled. If you require nucleotide alignment, you can convert back to the original nucleotides afterwards - but this is more likely to be required with multiple alignment than with pairwise (and for multiple alignments can be achieved with EMBOSS tranalign). Best regards, Daniel -- Daniel Barker http://bio.st-andrews.ac.uk/staff/db60.htm The University of St Andrews is a charity registered in Scotland : No SC013532 From jmeador45 at mac.com Mon Jan 31 04:49:38 2011 From: jmeador45 at mac.com (Jim Meador) Date: Sun, 30 Jan 2011 23:49:38 -0500 Subject: [EMBOSS] can't install emboss 6.3.1 in mac os x 10.6 Message-ID: <0192CFFE-D4EB-4FDB-B09D-59AB292ED208@mac.com> Hi Everyone, I am wanting to pgrade EMBOSS 6.3.1 on Mac OS X 10.6.6 (MacBook Pro 2.2 GHz, 4GB) from EMBOSS 6.2.0 that was installed in Leopoard (10.5) before I upgraded to Snow Leopard (10.6) and it seems to not do the make process correctly, where in the plplot directory, the .libs directory does not get created, so when I do sudo make install, it fails with these error messages: Making install in plplot make[1]: Entering directory `/Users/jmeador/newApps/MolBioChemSoftware/MolBioGeneral/EMBOSS/EMBOSS-6.3.1/plplot' Making install in lib make[2]: Entering directory `/Users/jmeador/newApps/MolBioChemSoftware/MolBioGeneral/EMBOSS/EMBOSS-6.3.1/plplot/lib' make[3]: Entering directory `/Users/jmeador/newApps/MolBioChemSoftware/MolBioGeneral/EMBOSS/EMBOSS-6.3.1/plplot/lib' make[3]: Nothing to be done for `install-exec-am'. test -z "/usr/local/share/EMBOSS" || ../.././install-sh -c -d "/usr/local/share/EMBOSS" /usr/bin/install -c -m 644 plstnd5.fnt plxtnd5.fnt '/usr/local/share/EMBOSS' make[3]: Leaving directory `/Users/jmeador/newApps/MolBioChemSoftware/MolBioGeneral/EMBOSS/EMBOSS-6.3.1/plplot/lib' make[2]: Leaving directory `/Users/jmeador/newApps/MolBioChemSoftware/MolBioGeneral/EMBOSS/EMBOSS-6.3.1/plplot/lib' make[2]: Entering directory `/Users/jmeador/newApps/MolBioChemSoftware/MolBioGeneral/EMBOSS/EMBOSS-6.3.1/plplot' make[3]: Entering directory `/Users/jmeador/newApps/MolBioChemSoftware/MolBioGeneral/EMBOSS/EMBOSS-6.3.1/plplot' test -z "/usr/local/lib" || .././install-sh -c -d "/usr/local/lib" /bin/sh ../libtool --mode=install /usr/bin/install -c libeplplot.la '/usr/local/lib' libtool: install: /usr/bin/install -c .libs/libeplplot.3.dylib /usr/local/lib/libeplplot.3.dylib install: .libs/libeplplot.3.dylib: No such file or directory make[3]: *** [install-libLTLIBRARIES] Error 71 make[3]: Leaving directory `/Users/jmeador/newApps/MolBioChemSoftware/MolBioGeneral/EMBOSS/EMBOSS-6.3.1/plplot' make[2]: *** [install-am] Error 2 make[2]: Leaving directory `/Users/jmeador/newApps/MolBioChemSoftware/MolBioGeneral/EMBOSS/EMBOSS-6.3.1/plplot' make[1]: *** [install-recursive] Error 1 make[1]: Leaving directory `/Users/jmeador/newApps/MolBioChemSoftware/MolBioGeneral/EMBOSS/EMBOSS-6.3.1/plplot' make: *** [install-recursive] Error 1 When I look in the source directory, /EMBOSS-6.3.1/plplot/ there is no .libs directory as there is in another installation on a newer MacBook Pro that I was able to successfully install this same software (10.6.6, 2.6 GHz, 8GB). My setup is a little more complicated than I would like, since I have installed the eBiotools-3.0.1-leopard software which sets up an older version of emboss 5.0.0 within a /usr/ebiotools/ directory and uses a very nice gui program to access these older emboss programs, called "eBioX" (and I don't want to lose this). So I have been installing the newer 6.x version of emboss to use at the commandline and with kemboss, both of which work, sort of. I have to play with the environment variables to get the text output programs to work, but I cannot get the graphics to work from various emboss programs that try to make graphs, such as "charge". The text-based programs work but I want to get the graphics working as well as it does from the ebiotools versions and will probably need to re-make emboss 6.3.1 after (re)installing gd and libpng. However, on this mac, neither ps nor x11 work. On the newer mac, with 6.3.1 installed, I don't have png or gif support, but I can at least get graphs in ps and x11 to work. Does anyone have any ideas of what I may be doing wrong? Is it possible that some environment variable could be causing this? Any ideas will be greatly appreciated. Thanks, Jim From idrummon at receptor.mgh.harvard.edu Mon Jan 31 16:05:06 2011 From: idrummon at receptor.mgh.harvard.edu (Iain Drummond) Date: Mon, 31 Jan 2011 11:05:06 -0500 Subject: [EMBOSS] can't install emboss 6.3.1 in mac os x 10.6 In-Reply-To: <0192CFFE-D4EB-4FDB-B09D-59AB292ED208@mac.com> Message-ID: I seem to remember that i could bypass this issue by configuring EMBOSS to install without x11. I realize that's not what you want to do. I think the problem stems from the directory structure Apple uses for x11; i.e. Its not where EMBOSS thinks it is. Maybe Apple put xll in a new place with 10.6? Iain Drummond On 1/30/11 11:49 PM, "Jim Meador" wrote: > Hi Everyone, > > I am wanting to pgrade EMBOSS 6.3.1 on Mac OS X 10.6.6 (MacBook Pro 2.2 GHz, > 4GB) from EMBOSS 6.2.0 that was installed in Leopoard (10.5) before I upgraded > to Snow Leopard (10.6) and it seems to not do the make process correctly, > where in the plplot directory, the .libs directory does not get created, so > when I do sudo make install, it fails with these error messages: > > Making install in plplot > make[1]: Entering directory > `/Users/jmeador/newApps/MolBioChemSoftware/MolBioGeneral/EMBOSS/EMBOSS-6.3.1/p > lplot' > Making install in lib > make[2]: Entering directory > `/Users/jmeador/newApps/MolBioChemSoftware/MolBioGeneral/EMBOSS/EMBOSS-6.3.1/p > lplot/lib' > make[3]: Entering directory > `/Users/jmeador/newApps/MolBioChemSoftware/MolBioGeneral/EMBOSS/EMBOSS-6.3.1/p > lplot/lib' > make[3]: Nothing to be done for `install-exec-am'. > test -z "/usr/local/share/EMBOSS" || ../.././install-sh -c -d > "/usr/local/share/EMBOSS" > /usr/bin/install -c -m 644 plstnd5.fnt plxtnd5.fnt '/usr/local/share/EMBOSS' > make[3]: Leaving directory > `/Users/jmeador/newApps/MolBioChemSoftware/MolBioGeneral/EMBOSS/EMBOSS-6.3.1/p > lplot/lib' > make[2]: Leaving directory > `/Users/jmeador/newApps/MolBioChemSoftware/MolBioGeneral/EMBOSS/EMBOSS-6.3.1/p > lplot/lib' > make[2]: Entering directory > `/Users/jmeador/newApps/MolBioChemSoftware/MolBioGeneral/EMBOSS/EMBOSS-6.3.1/p > lplot' > make[3]: Entering directory > `/Users/jmeador/newApps/MolBioChemSoftware/MolBioGeneral/EMBOSS/EMBOSS-6.3.1/p > lplot' > test -z "/usr/local/lib" || .././install-sh -c -d "/usr/local/lib" > /bin/sh ../libtool --mode=install /usr/bin/install -c libeplplot.la > '/usr/local/lib' > libtool: install: /usr/bin/install -c .libs/libeplplot.3.dylib > /usr/local/lib/libeplplot.3.dylib > install: .libs/libeplplot.3.dylib: No such file or directory > make[3]: *** [install-libLTLIBRARIES] Error 71 > make[3]: Leaving directory > `/Users/jmeador/newApps/MolBioChemSoftware/MolBioGeneral/EMBOSS/EMBOSS-6.3.1/p > lplot' > make[2]: *** [install-am] Error 2 > make[2]: Leaving directory > `/Users/jmeador/newApps/MolBioChemSoftware/MolBioGeneral/EMBOSS/EMBOSS-6.3.1/p > lplot' > make[1]: *** [install-recursive] Error 1 > make[1]: Leaving directory > `/Users/jmeador/newApps/MolBioChemSoftware/MolBioGeneral/EMBOSS/EMBOSS-6.3.1/p > lplot' > make: *** [install-recursive] Error 1 > > When I look in the source directory, /EMBOSS-6.3.1/plplot/ there is no .libs > directory as there is in another installation on a newer MacBook Pro that I > was able to successfully install this same software (10.6.6, 2.6 GHz, 8GB). > > My setup is a little more complicated than I would like, since I have > installed the eBiotools-3.0.1-leopard software which sets up an older version > of emboss 5.0.0 within a /usr/ebiotools/ directory and uses a very nice gui > program to access these older emboss programs, called "eBioX" (and I don't > want to lose this). So I have been installing the newer 6.x version of emboss > to use at the commandline and with kemboss, both of which work, sort of. I > have to play with the environment variables to get the text output programs to > work, but I cannot get the graphics to work from various emboss programs that > try to make graphs, such as "charge". The text-based programs work but I want > to get the graphics working as well as it does from the ebiotools versions and > will probably need to re-make emboss 6.3.1 after (re)installing gd and libpng. > However, on this mac, neither ps nor x11 work. On the newer mac, with 6.3.1 > installed, I don't have png or gif support, but I can at least get g! > raphs in ps and x11 to work. > > Does anyone have any ideas of what I may be doing wrong? Is it possible that > some environment variable could be causing this? > > Any ideas will be greatly appreciated. > Thanks, > Jim > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. From frank.foerster at biozentrum.uni-wuerzburg.de Mon Jan 31 18:03:16 2011 From: frank.foerster at biozentrum.uni-wuerzburg.de (=?ISO-8859-15?Q?Frank_F=F6rster?=) Date: Mon, 31 Jan 2011 19:03:16 +0100 Subject: [EMBOSS] Batch alignments? Message-ID: <4D46F964.4010705@biozentrum.uni-wuerzburg.de> Dear Robin, Starting with release 6.2 the program needleall is included into the EMBOSS software package. This program allows the generation of all vs. all alignments of two sequence sets. So you can generate all alignments with just one program. See http://emboss.sourceforge.net/apps/release/6.3/emboss/apps/needleall.html for more information. The best thing about needleall is you do not need to write a Perl script, no matter if this is just a simple script. Maybe this can help you to find arguments for upgrading to a newer EMBOSS release. Best regards, Frank -- Dr. rer. net. Dipl. Biochem. Frank F?rster Department of Bioinformatics University of W?rzburg, Germany Fon: +49 931 - 31 84555 Fax: +49 931 - 31 84552 frank.foerster at biozentrum.uni-wuerzburg.de