From koenvanderdrift at gmail.com  Tue Aug  3 13:30:27 2010
From: koenvanderdrift at gmail.com (Koen van der Drift)
Date: Tue, 3 Aug 2010 13:30:27 -0400
Subject: [EMBOSS] accessing emboss ftp site
In-Reply-To: <FBBE6420-C5DA-4070-A67C-E7AC5A97F920@gmail.com>
References: <6F57C2D1-8927-420C-940C-C6EC0C62AABE@gmail.com>
	<4BD0DB9B.5050005@sonsorol.org>
	<l2o5cba6b9f1004230756gf04316acq8519b375ce29e0d8@mail.gmail.com>
	<4BD1C05D.5010109@sonsorol.org>
	<FBBE6420-C5DA-4070-A67C-E7AC5A97F920@gmail.com>
Message-ID: <AANLkTinz_A58G22oBr6cEj2aRrDmO6sWqCb45rRRGpMf@mail.gmail.com>

Ok, my mailing list delivery was set to 'disabled' so I never got any
replies :). So just replying to what I read in the archives.

I get the issue only with Transmit, when it executes the 'LIST -a'
command. So that may be different than the ls command that seems to be
working for Chris. Interestingly, in the most recent version of
Transmit, the LIST command is no longer used:

"LIST -a" is no longer sent every time regardless of hidden files setting

Since this is a major, paid update, I am still using the older
Transmit that executes the LIST command. Maybe there's a pref setting
that can turn this off, I'll look into that. When I use the command
line ftp, I have no problems, although I have not tried the LIST
command there. I am using OS 10.5.8, on a PPC.

- Koen.




On Fri, May 28, 2010 at 10:44 PM, Koen van der Drift
<koenvanderdrift at gmail.com> wrote:
> Hi Chris,
>
> Did you have a chance to look at this? Just tried again, and Transmit still
> won't let me access the emboss ftp site.
>
> Thanks,
>
> - Koen.
>
>
> On Apr 23, 2010, at 11:44 AM, Chris Dagdigian wrote:
>
>>
>> In the last few months the open-bio.org servers switched datacenters, IP
>> addresses and firewall/IDS appliances. Lots of juicy things to look at and
>> debug.
>>
>> Koen - if you have a chance can you send me the IP address that you are
>> using to connect from? I might be able to find some relevant log entries
>> with that info.
>>
>> -Chris
>>
>>
>>
>> Koen van der Drift wrote:
>>>
>>> Just for the record, it used to work with Transmit, this is only from
>>> the last few months.
>>>
>>> - Koen.
>>>
>>> On Thu, Apr 22, 2010 at 7:28 PM, Chris Dagdigian<dag at sonsorol.org>
>>> ?wrote:
>>>>
>>>> Might be an issue with the Juniper Netscreen firewall/IDS security
>>>> appliance
>>>> that sits upstream of the EMBOSS FTP server. I'll take a look at the
>>>> security logs and alerts.
>>>>
>>>> -Chris
>>>>
>>>>
>>>> Koen van der Drift wrote:
>>>>>
>>>>> Hi,
>>>>>
>>>>> For a while now I am unable to access the emboss ftp site using the OS
>>>>> X
>>>>> client Transmit. Loggin in works fine, but it chokes on the LIST
>>>>> command. I have no problems accessing it from the command line. I have
>>>>> added the output from Transmit below. I don't know if this is a
>>>>> Transmit
>>>>> or emboss issue, but just wanted to let you know.
>>>>>
>>>>> Thanks,
>>>>>
>>>>> - Koen.
>>>>>
>>>>>
>>>>> Transmit 3.6.9 Session Transcript
>>>>> LibNcFTP 3.2.1 (August 13, 2007) compiled for UNIX
>>>>> Uname: Darwin|exile.local|9.8.0|Darwin Kernel Version 9.8.0: Wed Jul 15
>>>>> 16:57:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_PPC|Power Macintosh
>>>>> 220: (vsFTPd 2.0.1)
>>>>> Connected to emboss.open-bio.org.
>>>>> Cmd: USER anonymous
>>>>> 331: Please specify the password.
>>>>> Cmd: PASS NcFTP@
>>>>> 230: Login successful.
>>>>> Cmd: TYPE A
>>>>> 200: Switching to ASCII mode.
>>>>> Logged in to emboss.open-bio.org as anonymous.
>>>>> Cmd: SYST
>>>>> 215: UNIX Type: L8
>>>>> Cmd: PWD
>>>>> 257: "/"
>>>>> Cmd: CWD /pub/EMBOSS/fixes
>>>>> 250: Directory successfully changed.
>>>>> Cmd: PWD
>>>>> 257: "/pub/EMBOSS/fixes"
>>>>> Cmd: PASV
>>>>> 227: Entering Passive Mode (208,94,50,58,83,232)
>>>>> Cmd: LIST -a
>>>>> Could not read reply from control connection -- timed out. (SReadline
>>>>> 1)
>>>>> 220: (vsFTPd 2.0.1)
>>>>> Connected to emboss.open-bio.org.
>>>>> Cmd: USER anonymous
>>>>> 331: Please specify the password.
>>>>> Cmd: PASS NcFTP@
>>>>> 230: Login successful.
>>>>> Logged in to emboss.open-bio.org as anonymous.
>>>>> Cmd: SYST
>>>>> 215: UNIX Type: L8
>>>>> Cmd: PWD
>>>>> 257: "/"
>>>>> Cmd: CWD /pub/EMBOSS/fixes
>>>>> 250: Directory successfully changed.
>>>>> Cmd: PWD
>>>>> 257: "/pub/EMBOSS/fixes"
>>>>> Cmd: PASV
>>>>> 227: Entering Passive Mode (208,94,50,58,222,100)
>>>>> Cmd: LIST -a
>>>>> Could not read reply from control connection -- timed out. (SReadline
>>>>> 1)
>>>>>
>>>>> _______________________________________________
>>>>> EMBOSS mailing list
>>>>> EMBOSS at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/emboss
>
>


From mathog at caltech.edu  Thu Aug  5 17:49:21 2010
From: mathog at caltech.edu (David Mathog)
Date: Thu, 05 Aug 2010 14:49:21 -0700
Subject: [EMBOSS] EMBOSS 6.3.1 available
Message-ID: <E1Oh8JV-0004BI-FU@mendel.bio.caltech.edu>

Never mind, find the answer through google.  The solution to this:

> libtool: Version mismatch error.  This is libtool 2.2.6b, but the
> libtool: definition of this LT_INIT comes from libtool 2.2.6.
> libtool: You should recreate aclocal.m4 with macros from libtool 2.2.6b
> libtool: and run autoconf again.

is 

  reautoconf -fi

and then start over.  At least the make has been running for several
minutes now and seems happy.

Regards,

David Mathog
mathog at caltech.edu
Manager, Sequence Analysis Facility, Biology Division, Caltech

From mathog at caltech.edu  Thu Aug  5 17:36:28 2010
From: mathog at caltech.edu (David Mathog)
Date: Thu, 05 Aug 2010 14:36:28 -0700
Subject: [EMBOSS] EMBOSS 6.3.1 available
Message-ID: <E1Oh872-0004Ad-Sk@mendel.bio.caltech.edu>

> EMBOSS 6.3.1 is now available

First time I have built EMBOSS on linux.  This is an x86_64 system,
Mandriva 2010.0, gcc 4.4.1.

Unpacked emboss, applied the patch, in the top directory:
./configure 
#seems happy
./make
#trundles and then does this

/bin/sh ../libtool --tag=CC   --mode=compile gcc -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"EMBOSS\"
-DVERSION=\"6.3.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1
-DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1
-DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1
-DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1
-DLT_OBJDIR=\".libs/\" -DHAVE_DIRENT_H=1 -DSTDC_HEADERS=1
-DHAVE_UNISTD_H=1 -DGETPGRP_VOID=1 -DHAVE_STRFTIME=1 -DHAVE_FORK=1
-DHAVE_VFORK=1 -DHAVE_WORKING_VFORK=1 -DHAVE_WORKING_FORK=1
-DHAVE_VPRINTF=1 -DHAVE_MEMMOVE=1 -DPLD_xwin=1 -DHAVE_LIBM=1 -DPLD_png=1
-I.  -I./ -I/usr/include/gd -DPREFIX=\"/usr/local\" -DBUILD_DIR=\".\"
-DDRV_DIR=\".\" -DEMBOSS_TOP=\"/home/lclsrc/EMBOSS\"  -DAJ_LinuxLF
-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE 
-DLENDIAN  -O2  -DNO_AUTH -D__amd64__   -MT pdfutils.lo -MD -MP -MF
.deps/pdfutils.Tpo -c -o pdfutils.lo pdfutils.c
libtool: Version mismatch error.  This is libtool 2.2.6b, but the
libtool: definition of this LT_INIT comes from libtool 2.2.6.
libtool: You should recreate aclocal.m4 with macros from libtool 2.2.6b
libtool: and run autoconf again.
make[2]: *** [pdfutils.lo] Error 63
make[2]: Leaving directory `/home/lclsrc/EMBOSS-6.3.1/plplot'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/lclsrc/EMBOSS-6.3.1/plplot'
make: *** [all-recursive] Error 1

Those libtool instructions might as well say "wave your magic wand and
turn lead into gold".  What, exactly, are the commands to run here?

More info (RPM package versions):
autoconf2.1-2.13-29mdv2010.0
autoconf-2.64-3mdv2010.0
libtool-base-2.2.6-6.1mdv2010.0
libtool-2.2.6-6.1mdv2010.0


Thanks,

David Mathog
mathog at caltech.edu
Manager, Sequence Analysis Facility, Biology Division, Caltech

From hliang at ksu.edu  Sun Aug  8 14:02:27 2010
From: hliang at ksu.edu (Hanquan Liang)
Date: Sun, 8 Aug 2010 13:02:27 -0500
Subject: [EMBOSS] retrieving entries from public database
Message-ID: <AANLkTi=bkZhsgQRF2A8mLHT77U6SFc7ObxSVrzhZvcY7@mail.gmail.com>

Hi everyone,

I'm new to EMBOSS.
After installing EMBOSS 6.10 in my ubuntu 10.04, 'showdb' showed no
database.  So I renamed 'emboss.default.template' to 'emboss.default',
and then a few test databases (coming with EMBOSS package, I assume)
were listed.  But still no accession to online database.  I know that
I can download and make a local one, but that will take up a lot of
space while just a small part of the entries are needed.

In 'emboss.default' I tried to add databases, but the user document of
EMBOSS is so out-of-date that I cannot follow it.  After several hours
of searching and testing, I gave up and decided to come here for help.
 How do you guys use EMBOSS to access online public database?  Can any
one show me some of the lines in your 'emboss.default'?

Thanks
H. Liang

From georgios at biotek.uio.no  Sun Aug  8 16:56:18 2010
From: georgios at biotek.uio.no (Georgios Magklaras)
Date: Sun, 08 Aug 2010 22:56:18 +0200
Subject: [EMBOSS] retrieving entries from public database
In-Reply-To: <AANLkTi=bkZhsgQRF2A8mLHT77U6SFc7ObxSVrzhZvcY7@mail.gmail.com>
References: <AANLkTi=bkZhsgQRF2A8mLHT77U6SFc7ObxSVrzhZvcY7@mail.gmail.com>
Message-ID: <4C5F19F2.30405@biotek.uio.no>

  On 08/08/2010 08:02 PM, Hanquan Liang wrote:
> ...  I know that
> I can download and make a local one, but that will take up a lot of
> space while just a small part of the entries are needed.
>
Depends on your data set. But I agree, if you do not need all of them, 
you should not have to get them down. However, note, that remote access 
method might not work properly sometimes and depending on the results of 
your query (10-1000 sequences) it is a slower method to get things down. 
If you require only some subsets of public databases, we can help you to 
create local filtered sets.

> In 'emboss.default' I tried to add databases, but the user document of
> EMBOSS is so out-of-date that I cannot follow it.
It is indeed. Note, however, that the EMBOSS team is working on 
releasing up-to-date documentation.

> After several hours
> of searching and testing, I gave up and decided to come here for help.
>   How do you guys use EMBOSS to access online public database?  Can any
> one show me some of the lines in your 'emboss.default'?
>
The best method is to use a well working public SRS server. EBI has one. 
To do that:
1)Modify your emboss.default file to contain an entry like the following:

DB special [
         type: N
         format: genbank
         method: entrez
         fields: "id acc gi sv des org key"
         url:    "http://www.ncbi.nlm.nih.gov/sites/gquery"
]

2)Save the emboss.default and make sure you have your Internet 
connection up.

3)Test your 'special' set with a query from the command line:
seqret special-des:H1N1

This should do the trick.

-- 
--
George Magklaras
Senior Systems Engineer/IT Manager
Biotek Center, University of Oslo
EMBnet TMPC Chair

http://folk.uio.no/georgios

Tel: +47 22840535




From hliang at ksu.edu  Sun Aug  8 18:49:17 2010
From: hliang at ksu.edu (Hanquan Liang)
Date: Sun, 8 Aug 2010 17:49:17 -0500
Subject: [EMBOSS] retrieving entries from public database
In-Reply-To: <4C5F19F2.30405@biotek.uio.no>
References: <AANLkTi=bkZhsgQRF2A8mLHT77U6SFc7ObxSVrzhZvcY7@mail.gmail.com>
	<4C5F19F2.30405@biotek.uio.no>
Message-ID: <AANLkTinv9iuq_ug7-XJxtrYEy1bZG2y4NdrCuqUDzmXf@mail.gmail.com>

Georgios,

Thanks for your reply.

I added your lines into the emboss.default.  It works.
But not for my own lines (I tried before subscribing this mailing list
for help) like:

DB embl [  type: N method: srswww format: embl release: "EBI"
  url: "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?%s"
  comment: "EMBL from the EBI" ]

DB swissprot [  type: P method: srswww format: swiss release: "EBI"
  url: "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz";
  comment: "SWISSPROT from the EBI" ]

DB sw [  type: P method: srswww format: swiss release: "EBI"
  url: "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz";
  dbalias: "SWISSPROT"
  comment: "SWISSPROT from the EBI" ]

DB uniprot [  type: P method: srswww format: swiss release: "EBI"
  url: "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz";
  comment: "UNIPROT from the EBI" ]


I'm confused how to use syntax.  should I put 'srswww' or 'url' or
'entrez' after 'method'?  and what kind of url should I put after
'url'?  should I include or omit '%s'?  It's difficult for a newbie
like me to understand.


On Sun, Aug 8, 2010 at 3:56 PM, Georgios Magklaras
<georgios at biotek.uio.no> wrote:
> ?On 08/08/2010 08:02 PM, Hanquan Liang wrote:
>>
>> ... ?I know that
>> I can download and make a local one, but that will take up a lot of
>> space while just a small part of the entries are needed.
>>
> Depends on your data set. But I agree, if you do not need all of them, you
> should not have to get them down. However, note, that remote access method
> might not work properly sometimes and depending on the results of your query
> (10-1000 sequences) it is a slower method to get things down. If you require
> only some subsets of public databases, we can help you to create local
> filtered sets.
>
>> In 'emboss.default' I tried to add databases, but the user document of
>> EMBOSS is so out-of-date that I cannot follow it.
>
> It is indeed. Note, however, that the EMBOSS team is working on releasing
> up-to-date documentation.
>
>> After several hours
>> of searching and testing, I gave up and decided to come here for help.
>> ?How do you guys use EMBOSS to access online public database? ?Can any
>> one show me some of the lines in your 'emboss.default'?
>>
> The best method is to use a well working public SRS server. EBI has one. To
> do that:
> 1)Modify your emboss.default file to contain an entry like the following:
>
> DB special [
> ? ? ? ?type: N
> ? ? ? ?format: genbank
> ? ? ? ?method: entrez
> ? ? ? ?fields: "id acc gi sv des org key"
> ? ? ? ?url: ? ?"http://www.ncbi.nlm.nih.gov/sites/gquery"
> ]
>
> 2)Save the emboss.default and make sure you have your Internet connection
> up.
>
> 3)Test your 'special' set with a query from the command line:
> seqret special-des:H1N1
>
> This should do the trick.
>
> --
> --
> George Magklaras
> Senior Systems Engineer/IT Manager
> Biotek Center, University of Oslo
> EMBnet TMPC Chair
>
> http://folk.uio.no/georgios
>
> Tel: +47 22840535
>
>
>
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss
>


From pmr at ebi.ac.uk  Mon Aug  9 04:04:38 2010
From: pmr at ebi.ac.uk (Peter Rice)
Date: Mon, 09 Aug 2010 09:04:38 +0100
Subject: [EMBOSS] retrieving entries from public database
In-Reply-To: <AANLkTinv9iuq_ug7-XJxtrYEy1bZG2y4NdrCuqUDzmXf@mail.gmail.com>
References: <AANLkTi=bkZhsgQRF2A8mLHT77U6SFc7ObxSVrzhZvcY7@mail.gmail.com>	<4C5F19F2.30405@biotek.uio.no>
	<AANLkTinv9iuq_ug7-XJxtrYEy1bZG2y4NdrCuqUDzmXf@mail.gmail.com>
Message-ID: <4C5FB696.5040704@ebi.ac.uk>

Dear Hanquan,

On 08/08/2010 23:49, Hanquan Liang wrote:
> Georgios,
>
> Thanks for your reply.
>
> I added your lines into the emboss.default.  It works.
> But not for my own lines (I tried before subscribing this mailing list
> for help) like:

Ah, the new user's worst fear. More than one problem.

> DB embl [  type: N method: srswww format: embl release: "EBI"
>    url: "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?%s"
>    comment: "EMBL from the EBI" ]

The "?%s" at the end of the URL is the problem. "%s" is used for method: 
url to include the sequence ID in the search. Srswww and othe rmethods 
know how to build specific SRS webserver queries.

> DB swissprot [  type: P method: srswww format: swiss release: "EBI"
>    url: "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz";
>    comment: "SWISSPROT from the EBI" ]

This time the problem is the stray ';' at tghe end of the url: ... this 
stops EMBOSS finding the trailing '"' and so tghe comment has been 
included in the URL.

> DB sw [  type: P method: srswww format: swiss release: "EBI"
>    url: "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz";
>    dbalias: "SWISSPROT"
>    comment: "SWISSPROT from the EBI" ]

That ';' again ... well done for gettig the dbalias right. dbalias: is 
required when the database name you choose is not the same as the name 
on the SRS server (embl and swissprot both exist on the server)

> DB uniprot [  type: P method: srswww format: swiss release: "EBI"
>    url: "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz";
>    comment: "UNIPROT from the EBI" ]

The ';' again. Uniprot exists so again no dbalias is needed.


We will try to improve our error messages in these cases so you can see 
more detail on why the query fails. We should be able to find some SRS 
error message where the entries are not found, and return more detail 
where the query fails completely.

Hope this helps, and please do ask again if you have more questions. The 
direct address for the emboss team is emboss-bug at emboss.open-bio.org

Peter Rice

From georgios at biotek.uio.no  Mon Aug  9 04:59:30 2010
From: georgios at biotek.uio.no (Georgios Magklaras)
Date: Mon, 09 Aug 2010 10:59:30 +0200
Subject: [EMBOSS] retrieving entries from public database
In-Reply-To: <AANLkTinv9iuq_ug7-XJxtrYEy1bZG2y4NdrCuqUDzmXf@mail.gmail.com>
References: <AANLkTi=bkZhsgQRF2A8mLHT77U6SFc7ObxSVrzhZvcY7@mail.gmail.com>	<4C5F19F2.30405@biotek.uio.no>
	<AANLkTinv9iuq_ug7-XJxtrYEy1bZG2y4NdrCuqUDzmXf@mail.gmail.com>
Message-ID: <4C5FC372.8060102@biotek.uio.no>

  On 08/09/2010 12:49 AM, Hanquan Liang wrote:
> DB sw [  type: P method: srswww format: swiss release: "EBI"
>    url:"http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz";
>    dbalias: "SWISSPROT"
>    comment: "SWISSPROT from the EBI" ]

(the example I have you was an Entrez method example, as I thought you 
would be more familiar with genbank than embl. But the methods are similar)

OK, most the entries using the EBI SRS server will not work, due to the
;
symbol you have after the double quotes.

Generally, the method directive should be srswww. Be careful, however, 
because it is unclear to me whether the srswww can return multiple 
results. The 'entrez' method can.

-- 
--
George Magklaras
Senior Systems Engineer/IT Manager
Biotek Center, University of Oslo
EMBnet TMPC Chair

http://folk.uio.no/georgios

Tel: +47 22840535




From ajb at ebi.ac.uk  Tue Aug 10 06:16:52 2010
From: ajb at ebi.ac.uk (ajb at ebi.ac.uk)
Date: Tue, 10 Aug 2010 11:16:52 +0100 (BST)
Subject: [EMBOSS] Patch 1-4 available for EMBOSS-6.3.1
Message-ID: <41496.86.26.12.63.1281435412.squirrel@webmail.ebi.ac.uk>

The latest patch for EMBOSS-6.3.1 is available from:

  ftp://emboss.open-bio.org/pub/EMBOSS/fixes/patches/patch-1-4.gz

(and the corresponding discrete files in the directory above). The
latest mEMBOSS containing these fixes is available at:

  ftp://emboss.open-bio.org/pub/EMBOSS/windows/mEMBOSS-6.3.1.2-setup.exe

This fixes:

    Loading of two Ensembl sequences without the need to reload the
    registry.

    Correction the registration of the Ensembl Genomes database.

    Ensembl Genomes identifiers for species without a stable identifier
    should work. If the identifier does not obey a stable identifier
    pattern then it is matched against Exons, Transcripts and
    Translations in exactly that order.

It also corrects a side-effect of the first patch whereby the build
could fail with a libtool error if the host system had the latest
libtool installed.

Note that direct retrieval from the Ensembl server is still a
work in progress. As an example of its use, the following
commands will work using the example definitions in the
emboss.default.template file (no action required for mEMBOSS users).

seqret ensembl:human:ENST00000262160
seqret 'ensemblgenomes:Escherichia coli K12:EBESCT00000004007'
seqret 'ensemblgenomes:Escherichia coli DH10B:EBESCT00000011809'
seqret 'ensemblgenomes:Schizosaccharomyces pombe:SPAC2F7.03c-1'

(Quotes used when space characters are part of the retrieval term)

Alan



From n.binns at ed.ac.uk  Wed Aug 11 09:31:09 2010
From: n.binns at ed.ac.uk (Nigel Binns)
Date: Wed, 11 Aug 2010 14:31:09 +0100
Subject: [EMBOSS] Jemboss/EMBOSS can't find the external clustalw binary
Message-ID: <4C62A61D.3020500@ed.ac.uk>

  Hi All,

Please can anyone tell me why my installation of Jemboss (EMBOSS v6.3.1 
patch v1-4) can't find the external clustal binary and how to correct 
this. When I run a multiple sequence alignment using emma, I get the 
following output:

Died: emma uses external program 'clustalw' which is not in the PATH or 
defined as EMBOSS_CLUSTALW

I can confirm that my jemboss.properties file 
($EMBOSS_ROOT/share/EMBOSS/jemboss/resource/jemboss.properties) 
correctly points to the root directories of the clustalw and primer3 
binaries e.g.:

embossPath=/path/to/clustal:/path/to/primer3

Can I also expect the same problem with the external primer3 binary? 
Presumably the same solution for clustal will work for primer3?

Also, and I suspect I know the answer to this question, I'm attempting 
to input a test file into emma with the following contents:


SWISSPROT:PA1_HUMAN
SWISSPROT:PAX1_HUMAN
SWISSPROT:PAX2_HUMAN
SWISSPROT:PAX3_HUMAN
SWISSPROT:PAX4_HUMAN
SWISSPROT:PAX5_HUMAN
SWISSPROT:PAX6_HUMAN
SWISSPROT:PAX7_HUMAN
SWISSPROT:PAX8_HUMAN
SWISSPROT:PAX9_HUMAN
SWISSPROT:PAXI1_HUMAN

I pre-pended the path to this file with an @ to indicate that it's a 
list file e.g.:

@C:\path\to\multiple\sequence\alignment\file.sw

Am I correct in assuming that even when I've resolved the path issue to 
the clustalw binary, I need a locally installed database (or URL to an 
external database) for this analysis to run successfully? If so, how do 
I prepare/install/configure my system to access this database (Swiss-Prot)?

Many thanks for your time and help.

Best regards,

Nigel Binns


-- 
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.


From biopython at maubp.freeserve.co.uk  Wed Aug 11 11:02:40 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Wed, 11 Aug 2010 16:02:40 +0100
Subject: [EMBOSS] Jemboss/EMBOSS can't find the external clustalw binary
In-Reply-To: <4C62A61D.3020500@ed.ac.uk>
References: <4C62A61D.3020500@ed.ac.uk>
Message-ID: <AANLkTi=FBuhvoavXrLPx5Sc+GjMiiF_AkPOeZTuQ1+wx@mail.gmail.com>

On Wed, Aug 11, 2010 at 2:31 PM, Nigel Binns <n.binns at ed.ac.uk> wrote:
>
> ?Hi All,
>
> Please can anyone tell me why my installation of Jemboss (EMBOSS v6.3.1
> patch v1-4) can't find the external clustal binary and how to correct this.
> When I run a multiple sequence alignment using emma, I get the following
> output:
>
> Died: emma uses external program 'clustalw' which is not in the PATH or
> defined as EMBOSS_CLUSTALW
>
> I can confirm that my jemboss.properties file
> ($EMBOSS_ROOT/share/EMBOSS/jemboss/resource/jemboss.properties) correctly
> points to the root directories of the clustalw and primer3 binaries e.g.:
>
> embossPath=/path/to/clustal:/path/to/primer3

Have you got clustalw 1.x or 2.x installed? The binary names differ,
clustalw.exe versus clustalw2.exe (no extension on Unix/Linux), and
perhaps EMBOSS only expects the former?

Have you tried setting the EMBOSS_CLUSTALW variable?

Peter


From n.binns at ed.ac.uk  Thu Aug 12 04:17:23 2010
From: n.binns at ed.ac.uk (Nigel Binns)
Date: Thu, 12 Aug 2010 09:17:23 +0100
Subject: [EMBOSS] Jemboss/EMBOSS can't find the external clustalw binary
In-Reply-To: <AANLkTi=FBuhvoavXrLPx5Sc+GjMiiF_AkPOeZTuQ1+wx@mail.gmail.com>
References: <4C62A61D.3020500@ed.ac.uk>
	<AANLkTi=FBuhvoavXrLPx5Sc+GjMiiF_AkPOeZTuQ1+wx@mail.gmail.com>
Message-ID: <4C63AE13.5000901@ed.ac.uk>

  Hi Peter,

Many thanks for your reply. I have ClustalW v2 installed (v2.0.12 - the 
latest release). The binary is named clustalw2. However, as I understand 
it, when running the Jemboss installation script, you are asked to 
provide the root directory that contains the clustalw binary rather than 
the name of the actual binary i.e /path/to/clustal/root/ rather than 
/path/to/clustal/root/clustalw2 or have I got that wrong?

The same issue applies to my installation of Primer3 ( latest release - 
3-2.2.2-beta). The binary name is primer3_core. I get this error when I 
try to run eprimer3.

Error   application terminated

     Died: eprimer3 uses external program 'primer3_core' which is not in 
the PATH or defined as EMBOSS_PRIMER3_CORE
          Part of the 'primer3' package, version 3.0, available from the
          Whitehead Institute. See: http://primer3.sourceforge.net/

Please can you tell me what file I should set the EMBOSS_CLUSTALW and 
EMBOSS_PRIMER3_CORE variables in.

Many thanks for your help.

Nigel





On 11/08/2010 16:02, Peter wrote:
> On Wed, Aug 11, 2010 at 2:31 PM, Nigel Binns<n.binns at ed.ac.uk>  wrote:
>>   Hi All,
>>
>> Please can anyone tell me why my installation of Jemboss (EMBOSS v6.3.1
>> patch v1-4) can't find the external clustal binary and how to correct this.
>> When I run a multiple sequence alignment using emma, I get the following
>> output:
>>
>> Died: emma uses external program 'clustalw' which is not in the PATH or
>> defined as EMBOSS_CLUSTALW
>>
>> I can confirm that my jemboss.properties file
>> ($EMBOSS_ROOT/share/EMBOSS/jemboss/resource/jemboss.properties) correctly
>> points to the root directories of the clustalw and primer3 binaries e.g.:
>>
>> embossPath=/path/to/clustal:/path/to/primer3
> Have you got clustalw 1.x or 2.x installed? The binary names differ,
> clustalw.exe versus clustalw2.exe (no extension on Unix/Linux), and
> perhaps EMBOSS only expects the former?
>
> Have you tried setting the EMBOSS_CLUSTALW variable?
>
> Peter
>

-- 
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.


From jmuehlis at uni-muenster.de  Thu Aug 12 04:00:01 2010
From: jmuehlis at uni-muenster.de (=?ISO-8859-1?Q?J=F6rg_M=FChlisch?=)
Date: Thu, 12 Aug 2010 10:00:01 +0200
Subject: [EMBOSS] emboss update on ubuntu fails
Message-ID: <1281600001.6720.27.camel@opossum>

Hi All,

while updating emboss using synaptic I ran into a problem. I use

http://envgen.nox.ac.uk/bio-linux unstable bio-linux as package source.

On ubuntu 8.04 emboss-data and emboss-doc were upgraded to 6.3.1-3, but
emboss-lib was not updated from 6.0.1-11 and emboss was deinstalled, but
not replaced by 6.3.1-3. The column newest Version remains at 6.0.1-3
for both.
If I try to install the dependencies are not fullfilled:
emboss:
  H?ngt ab: ?emboss-data (=6.0.1-11)?, aber es wird ?6.3.1-3?
installiert.
(Depends on: ?emboss-data (=6.0.1-11)?, but ?6.3.1-3? will be
installed.)

On another 8.04 system the situation is the same, although emboss was
not deinstalled. If I update the packages I can not update emboss-data
(already installed), because the authenticity of the package can not be
confirmed.

Hope this will help to solve the problem.

For my situation the only solution I found would be to force
installation of 6.0.1-3 for all packages to fulfill the dependencies or
to deinstall and reinstall all packages, but I m afraid this will not
work, because the packages were not found.

I would appreciate any help to solve this problem.

Thanks

Jorg


-- 
Dr. J?rg M?hlisch

Klinik- und Poliklinik f?r Kinder und Jugendmedizin
P?diatrische H?matologie und Onkologie

Albert-Schweitzer-Str. 33
48129 M?nster

Tel.: +49-251/83-52491
Fax.: +49-251/83-55740



From biopython at maubp.freeserve.co.uk  Thu Aug 12 05:19:33 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Thu, 12 Aug 2010 10:19:33 +0100
Subject: [EMBOSS] Jemboss/EMBOSS can't find the external clustalw binary
In-Reply-To: <4C63AE13.5000901@ed.ac.uk>
References: <4C62A61D.3020500@ed.ac.uk>
	<AANLkTi=FBuhvoavXrLPx5Sc+GjMiiF_AkPOeZTuQ1+wx@mail.gmail.com>
	<4C63AE13.5000901@ed.ac.uk>
Message-ID: <AANLkTimz8C7i7AptwnegTCaa-k=ppan1P7HskVBjf7L0@mail.gmail.com>

On Thu, Aug 12, 2010 at 9:17 AM, Nigel Binns <n.binns at ed.ac.uk> wrote:
>
> ?Hi Peter,
>
> Many thanks for your reply. I have ClustalW v2 installed (v2.0.12 - the
> latest release). The binary is named clustalw2. However, as I understand it,
> when running the Jemboss installation script, you are asked to provide the
> root directory that contains the clustalw binary rather than the name of the
> actual binary i.e /path/to/clustal/root/ rather than
> /path/to/clustal/root/clustalw2 or have I got that wrong?

I was suggesting the problem could be EMBOSS only looks for clustalw
and not clustalw2.

> The same issue applies to my installation of Primer3 ( latest release -
> 3-2.2.2-beta). The binary name is primer3_core. I get this error when I try
> to run eprimer3.
>
> Error ? application terminated
>
> ? ?Died: eprimer3 uses external program 'primer3_core' which is not in the
> PATH or defined as EMBOSS_PRIMER3_CORE
> ? ? ? ? Part of the 'primer3' package, version 3.0, available from the
> ? ? ? ? Whitehead Institute. See: http://primer3.sourceforge.net/
>
> Please can you tell me what file I should set the EMBOSS_CLUSTALW and
> EMBOSS_PRIMER3_CORE variables in.

They are just environment variables (set up in the OS), but I haven't
ever used Jemboss so don't know how it would handle this.

>
> Many thanks for your help.
>
> Nigel

Peter C.


From btiwari at ceh.ac.uk  Thu Aug 12 05:06:40 2010
From: btiwari at ceh.ac.uk (Tiwari, Bela)
Date: Thu, 12 Aug 2010 10:06:40 +0100
Subject: [EMBOSS] emboss update on ubuntu fails
In-Reply-To: <1281600001.6720.27.camel@opossum>
References: <1281600001.6720.27.camel@opossum>
Message-ID: <1DCCED50D0696A498958BA6B254456E21B26D6EE90@nerckwmb1.ad.nerc.ac.uk>

Hello, 

This  is an issue specifically about the bio-linux-emboss package (which then calls on debian-med emboss package and the associated emboss-derivative packages).  Ie. nothing to do with the EMBOSS code itself. 

The central issue would appear to be the requirements of the emboss-related packages we supply,  which are appropriate for Ubuntu 10.04. In particular, the emboss-lib package depends on versions of packages that perhaps are not available for 8.04? (Without looking at this more closely, I couldn't say for sure).

However, as this issue is not an Emboss bug, it's probably best for me to get in touch with  J?rg directly rather than go into it in detail on this list.


cheers,

Bela

*************************
Dr. Bela Tiwari
Lead Bioinformatician
NERC Environmental
Bioinformatics Centre
http://nebc.nerc.ac.uk
tel: 01491 69 2705

Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB
*************************
________________________________________
From: emboss-bounces at lists.open-bio.org [emboss-bounces at lists.open-bio.org] On Behalf Of J?rg M?hlisch [jmuehlis at uni-muenster.de]
Sent: 12 August 2010 09:00
To: emboss at lists.open-bio.org
Subject: [EMBOSS] emboss update on ubuntu fails

Hi All,

while updating emboss using synaptic I ran into a problem. I use

http://envgen.nox.ac.uk/bio-linux unstable bio-linux as package source.

On ubuntu 8.04 emboss-data and emboss-doc were upgraded to 6.3.1-3, but
emboss-lib was not updated from 6.0.1-11 and emboss was deinstalled, but
not replaced by 6.3.1-3. The column newest Version remains at 6.0.1-3
for both.
If I try to install the dependencies are not fullfilled:
emboss:
  H?ngt ab: ?emboss-data (=6.0.1-11)?, aber es wird ?6.3.1-3?
installiert.
(Depends on: ?emboss-data (=6.0.1-11)?, but ?6.3.1-3? will be
installed.)

On another 8.04 system the situation is the same, although emboss was
not deinstalled. If I update the packages I can not update emboss-data
(already installed), because the authenticity of the package can not be
confirmed.

Hope this will help to solve the problem.

For my situation the only solution I found would be to force
installation of 6.0.1-3 for all packages to fulfill the dependencies or
to deinstall and reinstall all packages, but I m afraid this will not
work, because the packages were not found.

I would appreciate any help to solve this problem.

Thanks

Jorg


--
Dr. J?rg M?hlisch

Klinik- und Poliklinik f?r Kinder und Jugendmedizin
P?diatrische H?matologie und Onkologie

Albert-Schweitzer-Str. 33
48129 M?nster

Tel.: +49-251/83-52491
Fax.: +49-251/83-55740


_______________________________________________
EMBOSS mailing list
EMBOSS at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/emboss
-- 
This message (and any attachments) is for the recipient only. NERC
is subject to the Freedom of Information Act 2000 and the contents
of this email and any reply you make may be disclosed by NERC unless
it is exempt from release under the Act. Any material supplied to
NERC may be stored in an electronic records management system.



From sebastien.moretti at unil.ch  Thu Aug 12 05:47:22 2010
From: sebastien.moretti at unil.ch (=?ISO-8859-1?Q?S=E9bastien_Moretti?=)
Date: Thu, 12 Aug 2010 11:47:22 +0200
Subject: [EMBOSS] Last patched files not available on FTP
Message-ID: <4C63C32A.4020502@unil.ch>

Hi

last patched files are not available in
ftp://emboss.open-bio.org/pub/EMBOSS/fixes/


EMBOSS-6.3.1/ajax/graphics/ajgraph.c
EMBOSS-6.3.1/ajax/ensembl/ensregistry.c
EMBOSS-6.3.1/ajax/ajaxdb/ajseqdb.c.c


Could you add them on the FTP server ?

Do you mean ajseqdb.c.c or ajseqdb.c ?

Thanks
Regards

-- 
S?bastien Moretti
SIB Vital-IT EMBnet, Quartier Sorge - Genopode
CH-1015 Lausanne, Switzerland
Tel.: +41 (21) 692 4079/4221
http://www.vital-it.ch/ http://ch.embnet.org/ http://myhits.vital-it.ch/

From ajb at ebi.ac.uk  Thu Aug 12 09:24:57 2010
From: ajb at ebi.ac.uk (ajb at ebi.ac.uk)
Date: Thu, 12 Aug 2010 14:24:57 +0100 (BST)
Subject: [EMBOSS] Last patched files not available on FTP
In-Reply-To: <4C63C32A.4020502@unil.ch>
References: <4C63C32A.4020502@unil.ch>
Message-ID: <34953.86.26.12.63.1281619497.squirrel@webmail.ebi.ac.uk>

Hi,

Done.

ajseqdb.c

Alan


> Hi
>
> last patched files are not available in
> ftp://emboss.open-bio.org/pub/EMBOSS/fixes/
>
>
> EMBOSS-6.3.1/ajax/graphics/ajgraph.c
> EMBOSS-6.3.1/ajax/ensembl/ensregistry.c
> EMBOSS-6.3.1/ajax/ajaxdb/ajseqdb.c.c
>
>
> Could you add them on the FTP server ?
>
> Do you mean ajseqdb.c.c or ajseqdb.c ?
>
> Thanks
> Regards
>
> --
> S?bastien Moretti
> SIB Vital-IT EMBnet, Quartier Sorge - Genopode
> CH-1015 Lausanne, Switzerland
> Tel.: +41 (21) 692 4079/4221
> http://www.vital-it.ch/ http://ch.embnet.org/ http://myhits.vital-it.ch/
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss
>



From sebastien.moretti at unil.ch  Thu Aug 12 05:48:52 2010
From: sebastien.moretti at unil.ch (=?ISO-8859-1?Q?S=E9bastien_Moretti?=)
Date: Thu, 12 Aug 2010 11:48:52 +0200
Subject: [EMBOSS] Last patched files not available on FTP
In-Reply-To: <4C63C32A.4020502@unil.ch>
References: <4C63C32A.4020502@unil.ch>
Message-ID: <4C63C384.1020003@unil.ch>

Hoops !

Sorry, cache problem in my browser.
Files are here !

> Hi
>
> last patched files are not available in
> ftp://emboss.open-bio.org/pub/EMBOSS/fixes/
>
>
> EMBOSS-6.3.1/ajax/graphics/ajgraph.c
> EMBOSS-6.3.1/ajax/ensembl/ensregistry.c
> EMBOSS-6.3.1/ajax/ajaxdb/ajseqdb.c.c
>
>
> Could you add them on the FTP server ?
>
> Do you mean ajseqdb.c.c or ajseqdb.c ?
>
> Thanks
> Regards

-- 
S?bastien Moretti
SIB Vital-IT EMBnet, Quartier Sorge - Genopode
CH-1015 Lausanne, Switzerland
Tel.: +41 (21) 692 4079/4221
http://www.vital-it.ch/ http://ch.embnet.org/ http://myhits.vital-it.ch/

From karin.lagesen at bio.uio.no  Tue Aug 24 13:43:49 2010
From: karin.lagesen at bio.uio.no (Karin Lagesen)
Date: Tue, 24 Aug 2010 19:43:49 +0200
Subject: [EMBOSS] extract translations from genbank file
Message-ID: <4C7404D5.1050100@bio.uio.no>

Hello.

I am trying to extract the protein translations from a genbank file. I 
am managing to get the proteins, but I would like to get the information 
about the translation out from the file too.

Example:

      CDS             complement(93..1919)                  		


/translation="MTLENTSPNPSQISLNLSGGIALGAYMAGVCFELVRQARKDNSP
LLIDLITGASAGAMTGAITAYYLLNREISNTEYESQNILQRAWVEKADMKDIDTVFAI 
EDYRQVLNNLFKSQNESLLSQKGIKNIANLITENTDQLKVHQPLALVMTVTNLQGLLV
/product="hypothetical protein"

I have found two programs that could solve this problem. Coderet does 
give me the protein sequences, but the fasta description lines of the 
proteins are not easily relatable back to the genbank file.

>unknown_pro_1
MTLENTSPNPSQISLNLSGGIALGAYMAGVCFELVRQARKDNSPLLIDLITGASAGAMTG
AITAYYLLNREISNTEYESQNILQRAWVEKADMKDIDTVFAIEDYRQVLNNLFKSQNESL
LSQKGIKNIANLITENTDQLKVHQPLALVMTVTNLQGLLV

Extractfeat gives me sensible description lines, but for now I have not 
been able to make it give me the protein, and not the DNA sequence.

>scaffold00002_93_1919 [CDS] Contig scaffold00002
atgaccctagaaaatacctctcccaatcctagtcaaatttccctaaatttgtcgggagga
attgccctcggagcttatatggctggggtgtgttttgaattagttagacaagccagaaaa
gacaattctcccctgttaattgatttgattaccggagcatctgctggggcgatgaccgga
....


So. Are there any other programs, or options/switches to the ones that I 
have mentioned that I should be using?


TIA,

Karin

-- 
Karin Lagesen
Post Doc
Centre of Ecological and Evolutionary Synthesis (CEES)
Department of Biology
University of Oslo
P.O. Box 1066 - Blindern
N-0316 Oslo
Norway

From john.walshaw at bbsrc.ac.uk  Tue Aug 24 15:52:09 2010
From: john.walshaw at bbsrc.ac.uk (john walshaw (JIC))
Date: Tue, 24 Aug 2010 20:52:09 +0100
Subject: [EMBOSS] Authenticated Jemboss Server and .embossrc
Message-ID: <1BBF1266FD8E1B4781FB0DC46F0E553308ED1CC27A@nbiexch1.nbi.bbsrc.ac.uk>

Hello,

should a user's own EMBOSS configuration in ~/.embossrc be picked up by an Authenticated Jemboss Server running on the same host?

I'm having problems with this - i.e. some private databases defined in ~/.embossrc work fine from the command-line. The auth Jemboss Server also seems to work fine, as far as using a Jemboss client on a PC to log in and access (with read/write) remote files on the server host is concerned. I was expecting this to mean that the logged-in user's .embossrc would also be read, but it doesn't seem to happen as for example showdb doesn't list those databases, and nothing can access any sequence records from them.

This is using EMBOSS 6.0.1/Jemboss 1.5. Can you help?

best wishes,

John Walshaw




From david.bauer at bayerhealthcare.com  Wed Aug 25 02:17:56 2010
From: david.bauer at bayerhealthcare.com (david.bauer at bayerhealthcare.com)
Date: Wed, 25 Aug 2010 08:17:56 +0200
Subject: [EMBOSS] Antwort:  extract translations from genbank file
In-Reply-To: <4C7404D5.1050100@bio.uio.no>
Message-ID: <OF6F80E7B3.D8FF3E97-ONC125778A.00221B36-C125778A.00229A5D@bayer.de>

Hi Karin,

you can pipe the output from extractfeat into transeq to get the protein 
sequence:

extractfeat  mysequence.gb -type CDS -stdout | transeq -filter

HTH,

David.

emboss-bounces at lists.open-bio.org schrieb am 24/08/2010 19:43:49:

> Extractfeat gives me sensible description lines, but for now I have not 
> been able to make it give me the protein, and not the DNA sequence.
> 
> >scaffold00002_93_1919 [CDS] Contig scaffold00002
> atgaccctagaaaatacctctcccaatcctagtcaaatttccctaaatttgtcgggagga
> attgccctcggagcttatatggctggggtgtgttttgaattagttagacaagccagaaaa
> gacaattctcccctgttaattgatttgattaccggagcatctgctggggcgatgaccgga
> ....
> 
> 
> So. Are there any other programs, or options/switches to the ones that I 

> have mentioned that I should be using?
> 
> 
> TIA,
> 
> Karin
> 
> -- 
> Karin Lagesen
> Post Doc
> Centre of Ecological and Evolutionary Synthesis (CEES)
> Department of Biology
> University of Oslo
> P.O. Box 1066 - Blindern
> N-0316 Oslo
> Norway
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss

From aengus.stewart at cancer.org.uk  Tue Aug 31 05:07:10 2010
From: aengus.stewart at cancer.org.uk (Aengus Stewart)
Date: Tue, 31 Aug 2010 10:07:10 +0100
Subject: [EMBOSS] dbxflat problem
In-Reply-To: <6967ac4e0812100700s3708c00br7dbc606e79a6529c@mail.gmail.com>
References: <6967ac4e0812100700s3708c00br7dbc606e79a6529c@mail.gmail.com>
Message-ID: <4C7CC63E.2050007@cancer.org.uk>


Hi folks,

Not sure if I am doing something wrong but I am getting an error from 6.3.1 on Redhat EL5



dbxflat -verbose -idformat swiss -directory . -filenames "*.dat" -dbname trembl -dbresource trembl 
-release - -date 29/08/10 -fields id,acc,sv,des,key,org -outfile emboss.index.log
Index a flat file database using b+tree indices

    EMBOSS An error in ajindex.c at line 702:
Maximum retries (100) reached in btreeCacheFetch for page 1069056


Actually I am getting the same error with dbiflat as well.

dbxfasta -idformat gcgidacc -directory /data/INCOMING/nrprot -filenames nrprot.fasta -dbname nrprot 
-dbresource nrprot -release "-" -date 29/08/10 -fields "acc,sv,des" -outfile emboss.index.log
Index a fasta file database using b+tree indices

    EMBOSS An error in ajindex.c at line 702:
Maximum retries (100) reached in btreeCacheFetch for page 2774040576


Aengus


-- 
-----------------------------------------------------------------------
Aengus Stewart                                 Tel: +44 (0)20 7269 3679
Head of Bioinformatics and BioStatistics
CRUK London Research Institute
Lincoln's Inn Fields, Holborn, London, WC2A 3PX, UK
-----------------------------------------------------------------------

This electronic message contains information which may be privileged and
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From ajb at ebi.ac.uk  Tue Aug 31 06:52:20 2010
From: ajb at ebi.ac.uk (ajb at ebi.ac.uk)
Date: Tue, 31 Aug 2010 11:52:20 +0100 (BST)
Subject: [EMBOSS] dbxflat problem
In-Reply-To: <4C7CC63E.2050007@cancer.org.uk>
References: <6967ac4e0812100700s3708c00br7dbc606e79a6529c@mail.gmail.com>
	<4C7CC63E.2050007@cancer.org.uk>
Message-ID: <45956.86.26.12.63.1283251940.squirrel@webmail.ebi.ac.uk>

Hi Aengus,

Are you saying that it's restricted to RHEL5 or that it's the only
platform you've tried it on.

Assuming it's not restricted to RHEL5 then first check your RES
definitions in your emboss.default (or .embossrc) to verify that
the field lengths are not set too small.

If they look OK then you'd need to post us:

  a) Your RES definitions
  b) A URL/site and specify where we can get exactly the source
     data you are trying to index. Tell us of any modifications
     made to the data.
  c) The command lines used (already given below), plus any responses
     to any further prompts.

We could then attempt to reproduce the error.

HTH

Alan



>
> Hi folks,
>
> Not sure if I am doing something wrong but I am getting an error from
> 6.3.1 on Redhat EL5
>
>
>
> dbxflat -verbose -idformat swiss -directory . -filenames "*.dat" -dbname
> trembl -dbresource trembl
> -release - -date 29/08/10 -fields id,acc,sv,des,key,org -outfile
> emboss.index.log
> Index a flat file database using b+tree indices
>
>     EMBOSS An error in ajindex.c at line 702:
> Maximum retries (100) reached in btreeCacheFetch for page 1069056
>
>
> Actually I am getting the same error with dbiflat as well.
>
> dbxfasta -idformat gcgidacc -directory /data/INCOMING/nrprot -filenames
> nrprot.fasta -dbname nrprot
> -dbresource nrprot -release "-" -date 29/08/10 -fields "acc,sv,des"
> -outfile emboss.index.log
> Index a fasta file database using b+tree indices
>
>     EMBOSS An error in ajindex.c at line 702:
> Maximum retries (100) reached in btreeCacheFetch for page 2774040576
>
>
> Aengus
>
>
> --
> -----------------------------------------------------------------------
> Aengus Stewart                                 Tel: +44 (0)20 7269 3679
> Head of Bioinformatics and BioStatistics
> CRUK London Research Institute
> Lincoln's Inn Fields, Holborn, London, WC2A 3PX, UK
> -----------------------------------------------------------------------
>
> This electronic message contains information which may be privileged and
> confidential.  The information is intended to be for the use of the
> individual(s) or entity named above. Be aware that any third party
> disclosure, distribution, copying or use of this communication, without
> prior permission, is strictly prohibited.
>
> This communication is from Cancer Research UK. Our website is at
> www.cancerresearchuk.org. We are a registered charity in England and Wales
> (1089464) and in Scotland (SC041666) and a company limited by guarantee
> registered in England and Wales under number 4325234. Our registered
> address is 61 Lincoln's Inn Fields, London WC2A 3PX. Our central telephone
> number is 020 7242 0200.
>
>>From 1 October 2010 our registered address will be Angel Building, 407 St
>> John Street, London, EC1V 4AD.
>
> This communication and any attachments contain information which is
> confidential and may also be privileged.   It is for the exclusive use of
> the intended recipient(s).  If you are not the intended recipient(s)
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> arrive late or incomplete, or contain viruses.  We do not accept liability
> for any such matters or their consequences.  Anyone who communicates with
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>



From koenvanderdrift at gmail.com  Tue Aug  3 17:30:27 2010
From: koenvanderdrift at gmail.com (Koen van der Drift)
Date: Tue, 3 Aug 2010 13:30:27 -0400
Subject: [EMBOSS] accessing emboss ftp site
In-Reply-To: <FBBE6420-C5DA-4070-A67C-E7AC5A97F920@gmail.com>
References: <6F57C2D1-8927-420C-940C-C6EC0C62AABE@gmail.com>
	<4BD0DB9B.5050005@sonsorol.org>
	<l2o5cba6b9f1004230756gf04316acq8519b375ce29e0d8@mail.gmail.com>
	<4BD1C05D.5010109@sonsorol.org>
	<FBBE6420-C5DA-4070-A67C-E7AC5A97F920@gmail.com>
Message-ID: <AANLkTinz_A58G22oBr6cEj2aRrDmO6sWqCb45rRRGpMf@mail.gmail.com>

Ok, my mailing list delivery was set to 'disabled' so I never got any
replies :). So just replying to what I read in the archives.

I get the issue only with Transmit, when it executes the 'LIST -a'
command. So that may be different than the ls command that seems to be
working for Chris. Interestingly, in the most recent version of
Transmit, the LIST command is no longer used:

"LIST -a" is no longer sent every time regardless of hidden files setting

Since this is a major, paid update, I am still using the older
Transmit that executes the LIST command. Maybe there's a pref setting
that can turn this off, I'll look into that. When I use the command
line ftp, I have no problems, although I have not tried the LIST
command there. I am using OS 10.5.8, on a PPC.

- Koen.




On Fri, May 28, 2010 at 10:44 PM, Koen van der Drift
<koenvanderdrift at gmail.com> wrote:
> Hi Chris,
>
> Did you have a chance to look at this? Just tried again, and Transmit still
> won't let me access the emboss ftp site.
>
> Thanks,
>
> - Koen.
>
>
> On Apr 23, 2010, at 11:44 AM, Chris Dagdigian wrote:
>
>>
>> In the last few months the open-bio.org servers switched datacenters, IP
>> addresses and firewall/IDS appliances. Lots of juicy things to look at and
>> debug.
>>
>> Koen - if you have a chance can you send me the IP address that you are
>> using to connect from? I might be able to find some relevant log entries
>> with that info.
>>
>> -Chris
>>
>>
>>
>> Koen van der Drift wrote:
>>>
>>> Just for the record, it used to work with Transmit, this is only from
>>> the last few months.
>>>
>>> - Koen.
>>>
>>> On Thu, Apr 22, 2010 at 7:28 PM, Chris Dagdigian<dag at sonsorol.org>
>>> ?wrote:
>>>>
>>>> Might be an issue with the Juniper Netscreen firewall/IDS security
>>>> appliance
>>>> that sits upstream of the EMBOSS FTP server. I'll take a look at the
>>>> security logs and alerts.
>>>>
>>>> -Chris
>>>>
>>>>
>>>> Koen van der Drift wrote:
>>>>>
>>>>> Hi,
>>>>>
>>>>> For a while now I am unable to access the emboss ftp site using the OS
>>>>> X
>>>>> client Transmit. Loggin in works fine, but it chokes on the LIST
>>>>> command. I have no problems accessing it from the command line. I have
>>>>> added the output from Transmit below. I don't know if this is a
>>>>> Transmit
>>>>> or emboss issue, but just wanted to let you know.
>>>>>
>>>>> Thanks,
>>>>>
>>>>> - Koen.
>>>>>
>>>>>
>>>>> Transmit 3.6.9 Session Transcript
>>>>> LibNcFTP 3.2.1 (August 13, 2007) compiled for UNIX
>>>>> Uname: Darwin|exile.local|9.8.0|Darwin Kernel Version 9.8.0: Wed Jul 15
>>>>> 16:57:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_PPC|Power Macintosh
>>>>> 220: (vsFTPd 2.0.1)
>>>>> Connected to emboss.open-bio.org.
>>>>> Cmd: USER anonymous
>>>>> 331: Please specify the password.
>>>>> Cmd: PASS NcFTP@
>>>>> 230: Login successful.
>>>>> Cmd: TYPE A
>>>>> 200: Switching to ASCII mode.
>>>>> Logged in to emboss.open-bio.org as anonymous.
>>>>> Cmd: SYST
>>>>> 215: UNIX Type: L8
>>>>> Cmd: PWD
>>>>> 257: "/"
>>>>> Cmd: CWD /pub/EMBOSS/fixes
>>>>> 250: Directory successfully changed.
>>>>> Cmd: PWD
>>>>> 257: "/pub/EMBOSS/fixes"
>>>>> Cmd: PASV
>>>>> 227: Entering Passive Mode (208,94,50,58,83,232)
>>>>> Cmd: LIST -a
>>>>> Could not read reply from control connection -- timed out. (SReadline
>>>>> 1)
>>>>> 220: (vsFTPd 2.0.1)
>>>>> Connected to emboss.open-bio.org.
>>>>> Cmd: USER anonymous
>>>>> 331: Please specify the password.
>>>>> Cmd: PASS NcFTP@
>>>>> 230: Login successful.
>>>>> Logged in to emboss.open-bio.org as anonymous.
>>>>> Cmd: SYST
>>>>> 215: UNIX Type: L8
>>>>> Cmd: PWD
>>>>> 257: "/"
>>>>> Cmd: CWD /pub/EMBOSS/fixes
>>>>> 250: Directory successfully changed.
>>>>> Cmd: PWD
>>>>> 257: "/pub/EMBOSS/fixes"
>>>>> Cmd: PASV
>>>>> 227: Entering Passive Mode (208,94,50,58,222,100)
>>>>> Cmd: LIST -a
>>>>> Could not read reply from control connection -- timed out. (SReadline
>>>>> 1)
>>>>>
>>>>> _______________________________________________
>>>>> EMBOSS mailing list
>>>>> EMBOSS at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/emboss
>
>



From mathog at caltech.edu  Thu Aug  5 21:49:21 2010
From: mathog at caltech.edu (David Mathog)
Date: Thu, 05 Aug 2010 14:49:21 -0700
Subject: [EMBOSS] EMBOSS 6.3.1 available
Message-ID: <E1Oh8JV-0004BI-FU@mendel.bio.caltech.edu>

Never mind, find the answer through google.  The solution to this:

> libtool: Version mismatch error.  This is libtool 2.2.6b, but the
> libtool: definition of this LT_INIT comes from libtool 2.2.6.
> libtool: You should recreate aclocal.m4 with macros from libtool 2.2.6b
> libtool: and run autoconf again.

is 

  reautoconf -fi

and then start over.  At least the make has been running for several
minutes now and seems happy.

Regards,

David Mathog
mathog at caltech.edu
Manager, Sequence Analysis Facility, Biology Division, Caltech


From mathog at caltech.edu  Thu Aug  5 21:36:28 2010
From: mathog at caltech.edu (David Mathog)
Date: Thu, 05 Aug 2010 14:36:28 -0700
Subject: [EMBOSS] EMBOSS 6.3.1 available
Message-ID: <E1Oh872-0004Ad-Sk@mendel.bio.caltech.edu>

> EMBOSS 6.3.1 is now available

First time I have built EMBOSS on linux.  This is an x86_64 system,
Mandriva 2010.0, gcc 4.4.1.

Unpacked emboss, applied the patch, in the top directory:
./configure 
#seems happy
./make
#trundles and then does this

/bin/sh ../libtool --tag=CC   --mode=compile gcc -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"EMBOSS\"
-DVERSION=\"6.3.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1
-DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1
-DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1
-DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1
-DLT_OBJDIR=\".libs/\" -DHAVE_DIRENT_H=1 -DSTDC_HEADERS=1
-DHAVE_UNISTD_H=1 -DGETPGRP_VOID=1 -DHAVE_STRFTIME=1 -DHAVE_FORK=1
-DHAVE_VFORK=1 -DHAVE_WORKING_VFORK=1 -DHAVE_WORKING_FORK=1
-DHAVE_VPRINTF=1 -DHAVE_MEMMOVE=1 -DPLD_xwin=1 -DHAVE_LIBM=1 -DPLD_png=1
-I.  -I./ -I/usr/include/gd -DPREFIX=\"/usr/local\" -DBUILD_DIR=\".\"
-DDRV_DIR=\".\" -DEMBOSS_TOP=\"/home/lclsrc/EMBOSS\"  -DAJ_LinuxLF
-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE 
-DLENDIAN  -O2  -DNO_AUTH -D__amd64__   -MT pdfutils.lo -MD -MP -MF
.deps/pdfutils.Tpo -c -o pdfutils.lo pdfutils.c
libtool: Version mismatch error.  This is libtool 2.2.6b, but the
libtool: definition of this LT_INIT comes from libtool 2.2.6.
libtool: You should recreate aclocal.m4 with macros from libtool 2.2.6b
libtool: and run autoconf again.
make[2]: *** [pdfutils.lo] Error 63
make[2]: Leaving directory `/home/lclsrc/EMBOSS-6.3.1/plplot'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/lclsrc/EMBOSS-6.3.1/plplot'
make: *** [all-recursive] Error 1

Those libtool instructions might as well say "wave your magic wand and
turn lead into gold".  What, exactly, are the commands to run here?

More info (RPM package versions):
autoconf2.1-2.13-29mdv2010.0
autoconf-2.64-3mdv2010.0
libtool-base-2.2.6-6.1mdv2010.0
libtool-2.2.6-6.1mdv2010.0


Thanks,

David Mathog
mathog at caltech.edu
Manager, Sequence Analysis Facility, Biology Division, Caltech


From hliang at ksu.edu  Sun Aug  8 18:02:27 2010
From: hliang at ksu.edu (Hanquan Liang)
Date: Sun, 8 Aug 2010 13:02:27 -0500
Subject: [EMBOSS] retrieving entries from public database
Message-ID: <AANLkTi=bkZhsgQRF2A8mLHT77U6SFc7ObxSVrzhZvcY7@mail.gmail.com>

Hi everyone,

I'm new to EMBOSS.
After installing EMBOSS 6.10 in my ubuntu 10.04, 'showdb' showed no
database.  So I renamed 'emboss.default.template' to 'emboss.default',
and then a few test databases (coming with EMBOSS package, I assume)
were listed.  But still no accession to online database.  I know that
I can download and make a local one, but that will take up a lot of
space while just a small part of the entries are needed.

In 'emboss.default' I tried to add databases, but the user document of
EMBOSS is so out-of-date that I cannot follow it.  After several hours
of searching and testing, I gave up and decided to come here for help.
 How do you guys use EMBOSS to access online public database?  Can any
one show me some of the lines in your 'emboss.default'?

Thanks
H. Liang


From georgios at biotek.uio.no  Sun Aug  8 20:56:18 2010
From: georgios at biotek.uio.no (Georgios Magklaras)
Date: Sun, 08 Aug 2010 22:56:18 +0200
Subject: [EMBOSS] retrieving entries from public database
In-Reply-To: <AANLkTi=bkZhsgQRF2A8mLHT77U6SFc7ObxSVrzhZvcY7@mail.gmail.com>
References: <AANLkTi=bkZhsgQRF2A8mLHT77U6SFc7ObxSVrzhZvcY7@mail.gmail.com>
Message-ID: <4C5F19F2.30405@biotek.uio.no>

  On 08/08/2010 08:02 PM, Hanquan Liang wrote:
> ...  I know that
> I can download and make a local one, but that will take up a lot of
> space while just a small part of the entries are needed.
>
Depends on your data set. But I agree, if you do not need all of them, 
you should not have to get them down. However, note, that remote access 
method might not work properly sometimes and depending on the results of 
your query (10-1000 sequences) it is a slower method to get things down. 
If you require only some subsets of public databases, we can help you to 
create local filtered sets.

> In 'emboss.default' I tried to add databases, but the user document of
> EMBOSS is so out-of-date that I cannot follow it.
It is indeed. Note, however, that the EMBOSS team is working on 
releasing up-to-date documentation.

> After several hours
> of searching and testing, I gave up and decided to come here for help.
>   How do you guys use EMBOSS to access online public database?  Can any
> one show me some of the lines in your 'emboss.default'?
>
The best method is to use a well working public SRS server. EBI has one. 
To do that:
1)Modify your emboss.default file to contain an entry like the following:

DB special [
         type: N
         format: genbank
         method: entrez
         fields: "id acc gi sv des org key"
         url:    "http://www.ncbi.nlm.nih.gov/sites/gquery"
]

2)Save the emboss.default and make sure you have your Internet 
connection up.

3)Test your 'special' set with a query from the command line:
seqret special-des:H1N1

This should do the trick.

-- 
--
George Magklaras
Senior Systems Engineer/IT Manager
Biotek Center, University of Oslo
EMBnet TMPC Chair

http://folk.uio.no/georgios

Tel: +47 22840535





From hliang at ksu.edu  Sun Aug  8 22:49:17 2010
From: hliang at ksu.edu (Hanquan Liang)
Date: Sun, 8 Aug 2010 17:49:17 -0500
Subject: [EMBOSS] retrieving entries from public database
In-Reply-To: <4C5F19F2.30405@biotek.uio.no>
References: <AANLkTi=bkZhsgQRF2A8mLHT77U6SFc7ObxSVrzhZvcY7@mail.gmail.com>
	<4C5F19F2.30405@biotek.uio.no>
Message-ID: <AANLkTinv9iuq_ug7-XJxtrYEy1bZG2y4NdrCuqUDzmXf@mail.gmail.com>

Georgios,

Thanks for your reply.

I added your lines into the emboss.default.  It works.
But not for my own lines (I tried before subscribing this mailing list
for help) like:

DB embl [  type: N method: srswww format: embl release: "EBI"
  url: "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?%s"
  comment: "EMBL from the EBI" ]

DB swissprot [  type: P method: srswww format: swiss release: "EBI"
  url: "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz";
  comment: "SWISSPROT from the EBI" ]

DB sw [  type: P method: srswww format: swiss release: "EBI"
  url: "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz";
  dbalias: "SWISSPROT"
  comment: "SWISSPROT from the EBI" ]

DB uniprot [  type: P method: srswww format: swiss release: "EBI"
  url: "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz";
  comment: "UNIPROT from the EBI" ]


I'm confused how to use syntax.  should I put 'srswww' or 'url' or
'entrez' after 'method'?  and what kind of url should I put after
'url'?  should I include or omit '%s'?  It's difficult for a newbie
like me to understand.


On Sun, Aug 8, 2010 at 3:56 PM, Georgios Magklaras
<georgios at biotek.uio.no> wrote:
> ?On 08/08/2010 08:02 PM, Hanquan Liang wrote:
>>
>> ... ?I know that
>> I can download and make a local one, but that will take up a lot of
>> space while just a small part of the entries are needed.
>>
> Depends on your data set. But I agree, if you do not need all of them, you
> should not have to get them down. However, note, that remote access method
> might not work properly sometimes and depending on the results of your query
> (10-1000 sequences) it is a slower method to get things down. If you require
> only some subsets of public databases, we can help you to create local
> filtered sets.
>
>> In 'emboss.default' I tried to add databases, but the user document of
>> EMBOSS is so out-of-date that I cannot follow it.
>
> It is indeed. Note, however, that the EMBOSS team is working on releasing
> up-to-date documentation.
>
>> After several hours
>> of searching and testing, I gave up and decided to come here for help.
>> ?How do you guys use EMBOSS to access online public database? ?Can any
>> one show me some of the lines in your 'emboss.default'?
>>
> The best method is to use a well working public SRS server. EBI has one. To
> do that:
> 1)Modify your emboss.default file to contain an entry like the following:
>
> DB special [
> ? ? ? ?type: N
> ? ? ? ?format: genbank
> ? ? ? ?method: entrez
> ? ? ? ?fields: "id acc gi sv des org key"
> ? ? ? ?url: ? ?"http://www.ncbi.nlm.nih.gov/sites/gquery"
> ]
>
> 2)Save the emboss.default and make sure you have your Internet connection
> up.
>
> 3)Test your 'special' set with a query from the command line:
> seqret special-des:H1N1
>
> This should do the trick.
>
> --
> --
> George Magklaras
> Senior Systems Engineer/IT Manager
> Biotek Center, University of Oslo
> EMBnet TMPC Chair
>
> http://folk.uio.no/georgios
>
> Tel: +47 22840535
>
>
>
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss
>



From pmr at ebi.ac.uk  Mon Aug  9 08:04:38 2010
From: pmr at ebi.ac.uk (Peter Rice)
Date: Mon, 09 Aug 2010 09:04:38 +0100
Subject: [EMBOSS] retrieving entries from public database
In-Reply-To: <AANLkTinv9iuq_ug7-XJxtrYEy1bZG2y4NdrCuqUDzmXf@mail.gmail.com>
References: <AANLkTi=bkZhsgQRF2A8mLHT77U6SFc7ObxSVrzhZvcY7@mail.gmail.com>	<4C5F19F2.30405@biotek.uio.no>
	<AANLkTinv9iuq_ug7-XJxtrYEy1bZG2y4NdrCuqUDzmXf@mail.gmail.com>
Message-ID: <4C5FB696.5040704@ebi.ac.uk>

Dear Hanquan,

On 08/08/2010 23:49, Hanquan Liang wrote:
> Georgios,
>
> Thanks for your reply.
>
> I added your lines into the emboss.default.  It works.
> But not for my own lines (I tried before subscribing this mailing list
> for help) like:

Ah, the new user's worst fear. More than one problem.

> DB embl [  type: N method: srswww format: embl release: "EBI"
>    url: "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?%s"
>    comment: "EMBL from the EBI" ]

The "?%s" at the end of the URL is the problem. "%s" is used for method: 
url to include the sequence ID in the search. Srswww and othe rmethods 
know how to build specific SRS webserver queries.

> DB swissprot [  type: P method: srswww format: swiss release: "EBI"
>    url: "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz";
>    comment: "SWISSPROT from the EBI" ]

This time the problem is the stray ';' at tghe end of the url: ... this 
stops EMBOSS finding the trailing '"' and so tghe comment has been 
included in the URL.

> DB sw [  type: P method: srswww format: swiss release: "EBI"
>    url: "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz";
>    dbalias: "SWISSPROT"
>    comment: "SWISSPROT from the EBI" ]

That ';' again ... well done for gettig the dbalias right. dbalias: is 
required when the database name you choose is not the same as the name 
on the SRS server (embl and swissprot both exist on the server)

> DB uniprot [  type: P method: srswww format: swiss release: "EBI"
>    url: "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz";
>    comment: "UNIPROT from the EBI" ]

The ';' again. Uniprot exists so again no dbalias is needed.


We will try to improve our error messages in these cases so you can see 
more detail on why the query fails. We should be able to find some SRS 
error message where the entries are not found, and return more detail 
where the query fails completely.

Hope this helps, and please do ask again if you have more questions. The 
direct address for the emboss team is emboss-bug at emboss.open-bio.org

Peter Rice


From georgios at biotek.uio.no  Mon Aug  9 08:59:30 2010
From: georgios at biotek.uio.no (Georgios Magklaras)
Date: Mon, 09 Aug 2010 10:59:30 +0200
Subject: [EMBOSS] retrieving entries from public database
In-Reply-To: <AANLkTinv9iuq_ug7-XJxtrYEy1bZG2y4NdrCuqUDzmXf@mail.gmail.com>
References: <AANLkTi=bkZhsgQRF2A8mLHT77U6SFc7ObxSVrzhZvcY7@mail.gmail.com>	<4C5F19F2.30405@biotek.uio.no>
	<AANLkTinv9iuq_ug7-XJxtrYEy1bZG2y4NdrCuqUDzmXf@mail.gmail.com>
Message-ID: <4C5FC372.8060102@biotek.uio.no>

  On 08/09/2010 12:49 AM, Hanquan Liang wrote:
> DB sw [  type: P method: srswww format: swiss release: "EBI"
>    url:"http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz";
>    dbalias: "SWISSPROT"
>    comment: "SWISSPROT from the EBI" ]

(the example I have you was an Entrez method example, as I thought you 
would be more familiar with genbank than embl. But the methods are similar)

OK, most the entries using the EBI SRS server will not work, due to the
;
symbol you have after the double quotes.

Generally, the method directive should be srswww. Be careful, however, 
because it is unclear to me whether the srswww can return multiple 
results. The 'entrez' method can.

-- 
--
George Magklaras
Senior Systems Engineer/IT Manager
Biotek Center, University of Oslo
EMBnet TMPC Chair

http://folk.uio.no/georgios

Tel: +47 22840535





From ajb at ebi.ac.uk  Tue Aug 10 10:16:52 2010
From: ajb at ebi.ac.uk (ajb at ebi.ac.uk)
Date: Tue, 10 Aug 2010 11:16:52 +0100 (BST)
Subject: [EMBOSS] Patch 1-4 available for EMBOSS-6.3.1
Message-ID: <41496.86.26.12.63.1281435412.squirrel@webmail.ebi.ac.uk>

The latest patch for EMBOSS-6.3.1 is available from:

  ftp://emboss.open-bio.org/pub/EMBOSS/fixes/patches/patch-1-4.gz

(and the corresponding discrete files in the directory above). The
latest mEMBOSS containing these fixes is available at:

  ftp://emboss.open-bio.org/pub/EMBOSS/windows/mEMBOSS-6.3.1.2-setup.exe

This fixes:

    Loading of two Ensembl sequences without the need to reload the
    registry.

    Correction the registration of the Ensembl Genomes database.

    Ensembl Genomes identifiers for species without a stable identifier
    should work. If the identifier does not obey a stable identifier
    pattern then it is matched against Exons, Transcripts and
    Translations in exactly that order.

It also corrects a side-effect of the first patch whereby the build
could fail with a libtool error if the host system had the latest
libtool installed.

Note that direct retrieval from the Ensembl server is still a
work in progress. As an example of its use, the following
commands will work using the example definitions in the
emboss.default.template file (no action required for mEMBOSS users).

seqret ensembl:human:ENST00000262160
seqret 'ensemblgenomes:Escherichia coli K12:EBESCT00000004007'
seqret 'ensemblgenomes:Escherichia coli DH10B:EBESCT00000011809'
seqret 'ensemblgenomes:Schizosaccharomyces pombe:SPAC2F7.03c-1'

(Quotes used when space characters are part of the retrieval term)

Alan




From n.binns at ed.ac.uk  Wed Aug 11 13:31:09 2010
From: n.binns at ed.ac.uk (Nigel Binns)
Date: Wed, 11 Aug 2010 14:31:09 +0100
Subject: [EMBOSS] Jemboss/EMBOSS can't find the external clustalw binary
Message-ID: <4C62A61D.3020500@ed.ac.uk>

  Hi All,

Please can anyone tell me why my installation of Jemboss (EMBOSS v6.3.1 
patch v1-4) can't find the external clustal binary and how to correct 
this. When I run a multiple sequence alignment using emma, I get the 
following output:

Died: emma uses external program 'clustalw' which is not in the PATH or 
defined as EMBOSS_CLUSTALW

I can confirm that my jemboss.properties file 
($EMBOSS_ROOT/share/EMBOSS/jemboss/resource/jemboss.properties) 
correctly points to the root directories of the clustalw and primer3 
binaries e.g.:

embossPath=/path/to/clustal:/path/to/primer3

Can I also expect the same problem with the external primer3 binary? 
Presumably the same solution for clustal will work for primer3?

Also, and I suspect I know the answer to this question, I'm attempting 
to input a test file into emma with the following contents:


SWISSPROT:PA1_HUMAN
SWISSPROT:PAX1_HUMAN
SWISSPROT:PAX2_HUMAN
SWISSPROT:PAX3_HUMAN
SWISSPROT:PAX4_HUMAN
SWISSPROT:PAX5_HUMAN
SWISSPROT:PAX6_HUMAN
SWISSPROT:PAX7_HUMAN
SWISSPROT:PAX8_HUMAN
SWISSPROT:PAX9_HUMAN
SWISSPROT:PAXI1_HUMAN

I pre-pended the path to this file with an @ to indicate that it's a 
list file e.g.:

@C:\path\to\multiple\sequence\alignment\file.sw

Am I correct in assuming that even when I've resolved the path issue to 
the clustalw binary, I need a locally installed database (or URL to an 
external database) for this analysis to run successfully? If so, how do 
I prepare/install/configure my system to access this database (Swiss-Prot)?

Many thanks for your time and help.

Best regards,

Nigel Binns


-- 
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.



From biopython at maubp.freeserve.co.uk  Wed Aug 11 15:02:40 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Wed, 11 Aug 2010 16:02:40 +0100
Subject: [EMBOSS] Jemboss/EMBOSS can't find the external clustalw binary
In-Reply-To: <4C62A61D.3020500@ed.ac.uk>
References: <4C62A61D.3020500@ed.ac.uk>
Message-ID: <AANLkTi=FBuhvoavXrLPx5Sc+GjMiiF_AkPOeZTuQ1+wx@mail.gmail.com>

On Wed, Aug 11, 2010 at 2:31 PM, Nigel Binns <n.binns at ed.ac.uk> wrote:
>
> ?Hi All,
>
> Please can anyone tell me why my installation of Jemboss (EMBOSS v6.3.1
> patch v1-4) can't find the external clustal binary and how to correct this.
> When I run a multiple sequence alignment using emma, I get the following
> output:
>
> Died: emma uses external program 'clustalw' which is not in the PATH or
> defined as EMBOSS_CLUSTALW
>
> I can confirm that my jemboss.properties file
> ($EMBOSS_ROOT/share/EMBOSS/jemboss/resource/jemboss.properties) correctly
> points to the root directories of the clustalw and primer3 binaries e.g.:
>
> embossPath=/path/to/clustal:/path/to/primer3

Have you got clustalw 1.x or 2.x installed? The binary names differ,
clustalw.exe versus clustalw2.exe (no extension on Unix/Linux), and
perhaps EMBOSS only expects the former?

Have you tried setting the EMBOSS_CLUSTALW variable?

Peter



From n.binns at ed.ac.uk  Thu Aug 12 08:17:23 2010
From: n.binns at ed.ac.uk (Nigel Binns)
Date: Thu, 12 Aug 2010 09:17:23 +0100
Subject: [EMBOSS] Jemboss/EMBOSS can't find the external clustalw binary
In-Reply-To: <AANLkTi=FBuhvoavXrLPx5Sc+GjMiiF_AkPOeZTuQ1+wx@mail.gmail.com>
References: <4C62A61D.3020500@ed.ac.uk>
	<AANLkTi=FBuhvoavXrLPx5Sc+GjMiiF_AkPOeZTuQ1+wx@mail.gmail.com>
Message-ID: <4C63AE13.5000901@ed.ac.uk>

  Hi Peter,

Many thanks for your reply. I have ClustalW v2 installed (v2.0.12 - the 
latest release). The binary is named clustalw2. However, as I understand 
it, when running the Jemboss installation script, you are asked to 
provide the root directory that contains the clustalw binary rather than 
the name of the actual binary i.e /path/to/clustal/root/ rather than 
/path/to/clustal/root/clustalw2 or have I got that wrong?

The same issue applies to my installation of Primer3 ( latest release - 
3-2.2.2-beta). The binary name is primer3_core. I get this error when I 
try to run eprimer3.

Error   application terminated

     Died: eprimer3 uses external program 'primer3_core' which is not in 
the PATH or defined as EMBOSS_PRIMER3_CORE
          Part of the 'primer3' package, version 3.0, available from the
          Whitehead Institute. See: http://primer3.sourceforge.net/

Please can you tell me what file I should set the EMBOSS_CLUSTALW and 
EMBOSS_PRIMER3_CORE variables in.

Many thanks for your help.

Nigel





On 11/08/2010 16:02, Peter wrote:
> On Wed, Aug 11, 2010 at 2:31 PM, Nigel Binns<n.binns at ed.ac.uk>  wrote:
>>   Hi All,
>>
>> Please can anyone tell me why my installation of Jemboss (EMBOSS v6.3.1
>> patch v1-4) can't find the external clustal binary and how to correct this.
>> When I run a multiple sequence alignment using emma, I get the following
>> output:
>>
>> Died: emma uses external program 'clustalw' which is not in the PATH or
>> defined as EMBOSS_CLUSTALW
>>
>> I can confirm that my jemboss.properties file
>> ($EMBOSS_ROOT/share/EMBOSS/jemboss/resource/jemboss.properties) correctly
>> points to the root directories of the clustalw and primer3 binaries e.g.:
>>
>> embossPath=/path/to/clustal:/path/to/primer3
> Have you got clustalw 1.x or 2.x installed? The binary names differ,
> clustalw.exe versus clustalw2.exe (no extension on Unix/Linux), and
> perhaps EMBOSS only expects the former?
>
> Have you tried setting the EMBOSS_CLUSTALW variable?
>
> Peter
>

-- 
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.



From jmuehlis at uni-muenster.de  Thu Aug 12 08:00:01 2010
From: jmuehlis at uni-muenster.de (=?ISO-8859-1?Q?J=F6rg_M=FChlisch?=)
Date: Thu, 12 Aug 2010 10:00:01 +0200
Subject: [EMBOSS] emboss update on ubuntu fails
Message-ID: <1281600001.6720.27.camel@opossum>

Hi All,

while updating emboss using synaptic I ran into a problem. I use

http://envgen.nox.ac.uk/bio-linux unstable bio-linux as package source.

On ubuntu 8.04 emboss-data and emboss-doc were upgraded to 6.3.1-3, but
emboss-lib was not updated from 6.0.1-11 and emboss was deinstalled, but
not replaced by 6.3.1-3. The column newest Version remains at 6.0.1-3
for both.
If I try to install the dependencies are not fullfilled:
emboss:
  H?ngt ab: ?emboss-data (=6.0.1-11)?, aber es wird ?6.3.1-3?
installiert.
(Depends on: ?emboss-data (=6.0.1-11)?, but ?6.3.1-3? will be
installed.)

On another 8.04 system the situation is the same, although emboss was
not deinstalled. If I update the packages I can not update emboss-data
(already installed), because the authenticity of the package can not be
confirmed.

Hope this will help to solve the problem.

For my situation the only solution I found would be to force
installation of 6.0.1-3 for all packages to fulfill the dependencies or
to deinstall and reinstall all packages, but I m afraid this will not
work, because the packages were not found.

I would appreciate any help to solve this problem.

Thanks

Jorg


-- 
Dr. J?rg M?hlisch

Klinik- und Poliklinik f?r Kinder und Jugendmedizin
P?diatrische H?matologie und Onkologie

Albert-Schweitzer-Str. 33
48129 M?nster

Tel.: +49-251/83-52491
Fax.: +49-251/83-55740




From biopython at maubp.freeserve.co.uk  Thu Aug 12 09:19:33 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Thu, 12 Aug 2010 10:19:33 +0100
Subject: [EMBOSS] Jemboss/EMBOSS can't find the external clustalw binary
In-Reply-To: <4C63AE13.5000901@ed.ac.uk>
References: <4C62A61D.3020500@ed.ac.uk>
	<AANLkTi=FBuhvoavXrLPx5Sc+GjMiiF_AkPOeZTuQ1+wx@mail.gmail.com>
	<4C63AE13.5000901@ed.ac.uk>
Message-ID: <AANLkTimz8C7i7AptwnegTCaa-k=ppan1P7HskVBjf7L0@mail.gmail.com>

On Thu, Aug 12, 2010 at 9:17 AM, Nigel Binns <n.binns at ed.ac.uk> wrote:
>
> ?Hi Peter,
>
> Many thanks for your reply. I have ClustalW v2 installed (v2.0.12 - the
> latest release). The binary is named clustalw2. However, as I understand it,
> when running the Jemboss installation script, you are asked to provide the
> root directory that contains the clustalw binary rather than the name of the
> actual binary i.e /path/to/clustal/root/ rather than
> /path/to/clustal/root/clustalw2 or have I got that wrong?

I was suggesting the problem could be EMBOSS only looks for clustalw
and not clustalw2.

> The same issue applies to my installation of Primer3 ( latest release -
> 3-2.2.2-beta). The binary name is primer3_core. I get this error when I try
> to run eprimer3.
>
> Error ? application terminated
>
> ? ?Died: eprimer3 uses external program 'primer3_core' which is not in the
> PATH or defined as EMBOSS_PRIMER3_CORE
> ? ? ? ? Part of the 'primer3' package, version 3.0, available from the
> ? ? ? ? Whitehead Institute. See: http://primer3.sourceforge.net/
>
> Please can you tell me what file I should set the EMBOSS_CLUSTALW and
> EMBOSS_PRIMER3_CORE variables in.

They are just environment variables (set up in the OS), but I haven't
ever used Jemboss so don't know how it would handle this.

>
> Many thanks for your help.
>
> Nigel

Peter C.



From btiwari at ceh.ac.uk  Thu Aug 12 09:06:40 2010
From: btiwari at ceh.ac.uk (Tiwari, Bela)
Date: Thu, 12 Aug 2010 10:06:40 +0100
Subject: [EMBOSS] emboss update on ubuntu fails
In-Reply-To: <1281600001.6720.27.camel@opossum>
References: <1281600001.6720.27.camel@opossum>
Message-ID: <1DCCED50D0696A498958BA6B254456E21B26D6EE90@nerckwmb1.ad.nerc.ac.uk>

Hello, 

This  is an issue specifically about the bio-linux-emboss package (which then calls on debian-med emboss package and the associated emboss-derivative packages).  Ie. nothing to do with the EMBOSS code itself. 

The central issue would appear to be the requirements of the emboss-related packages we supply,  which are appropriate for Ubuntu 10.04. In particular, the emboss-lib package depends on versions of packages that perhaps are not available for 8.04? (Without looking at this more closely, I couldn't say for sure).

However, as this issue is not an Emboss bug, it's probably best for me to get in touch with  J?rg directly rather than go into it in detail on this list.


cheers,

Bela

*************************
Dr. Bela Tiwari
Lead Bioinformatician
NERC Environmental
Bioinformatics Centre
http://nebc.nerc.ac.uk
tel: 01491 69 2705

Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB
*************************
________________________________________
From: emboss-bounces at lists.open-bio.org [emboss-bounces at lists.open-bio.org] On Behalf Of J?rg M?hlisch [jmuehlis at uni-muenster.de]
Sent: 12 August 2010 09:00
To: emboss at lists.open-bio.org
Subject: [EMBOSS] emboss update on ubuntu fails

Hi All,

while updating emboss using synaptic I ran into a problem. I use

http://envgen.nox.ac.uk/bio-linux unstable bio-linux as package source.

On ubuntu 8.04 emboss-data and emboss-doc were upgraded to 6.3.1-3, but
emboss-lib was not updated from 6.0.1-11 and emboss was deinstalled, but
not replaced by 6.3.1-3. The column newest Version remains at 6.0.1-3
for both.
If I try to install the dependencies are not fullfilled:
emboss:
  H?ngt ab: ?emboss-data (=6.0.1-11)?, aber es wird ?6.3.1-3?
installiert.
(Depends on: ?emboss-data (=6.0.1-11)?, but ?6.3.1-3? will be
installed.)

On another 8.04 system the situation is the same, although emboss was
not deinstalled. If I update the packages I can not update emboss-data
(already installed), because the authenticity of the package can not be
confirmed.

Hope this will help to solve the problem.

For my situation the only solution I found would be to force
installation of 6.0.1-3 for all packages to fulfill the dependencies or
to deinstall and reinstall all packages, but I m afraid this will not
work, because the packages were not found.

I would appreciate any help to solve this problem.

Thanks

Jorg


--
Dr. J?rg M?hlisch

Klinik- und Poliklinik f?r Kinder und Jugendmedizin
P?diatrische H?matologie und Onkologie

Albert-Schweitzer-Str. 33
48129 M?nster

Tel.: +49-251/83-52491
Fax.: +49-251/83-55740


_______________________________________________
EMBOSS mailing list
EMBOSS at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/emboss
-- 
This message (and any attachments) is for the recipient only. NERC
is subject to the Freedom of Information Act 2000 and the contents
of this email and any reply you make may be disclosed by NERC unless
it is exempt from release under the Act. Any material supplied to
NERC may be stored in an electronic records management system.




From sebastien.moretti at unil.ch  Thu Aug 12 09:47:22 2010
From: sebastien.moretti at unil.ch (=?ISO-8859-1?Q?S=E9bastien_Moretti?=)
Date: Thu, 12 Aug 2010 11:47:22 +0200
Subject: [EMBOSS] Last patched files not available on FTP
Message-ID: <4C63C32A.4020502@unil.ch>

Hi

last patched files are not available in
ftp://emboss.open-bio.org/pub/EMBOSS/fixes/


EMBOSS-6.3.1/ajax/graphics/ajgraph.c
EMBOSS-6.3.1/ajax/ensembl/ensregistry.c
EMBOSS-6.3.1/ajax/ajaxdb/ajseqdb.c.c


Could you add them on the FTP server ?

Do you mean ajseqdb.c.c or ajseqdb.c ?

Thanks
Regards

-- 
S?bastien Moretti
SIB Vital-IT EMBnet, Quartier Sorge - Genopode
CH-1015 Lausanne, Switzerland
Tel.: +41 (21) 692 4079/4221
http://www.vital-it.ch/ http://ch.embnet.org/ http://myhits.vital-it.ch/


From ajb at ebi.ac.uk  Thu Aug 12 13:24:57 2010
From: ajb at ebi.ac.uk (ajb at ebi.ac.uk)
Date: Thu, 12 Aug 2010 14:24:57 +0100 (BST)
Subject: [EMBOSS] Last patched files not available on FTP
In-Reply-To: <4C63C32A.4020502@unil.ch>
References: <4C63C32A.4020502@unil.ch>
Message-ID: <34953.86.26.12.63.1281619497.squirrel@webmail.ebi.ac.uk>

Hi,

Done.

ajseqdb.c

Alan


> Hi
>
> last patched files are not available in
> ftp://emboss.open-bio.org/pub/EMBOSS/fixes/
>
>
> EMBOSS-6.3.1/ajax/graphics/ajgraph.c
> EMBOSS-6.3.1/ajax/ensembl/ensregistry.c
> EMBOSS-6.3.1/ajax/ajaxdb/ajseqdb.c.c
>
>
> Could you add them on the FTP server ?
>
> Do you mean ajseqdb.c.c or ajseqdb.c ?
>
> Thanks
> Regards
>
> --
> S?bastien Moretti
> SIB Vital-IT EMBnet, Quartier Sorge - Genopode
> CH-1015 Lausanne, Switzerland
> Tel.: +41 (21) 692 4079/4221
> http://www.vital-it.ch/ http://ch.embnet.org/ http://myhits.vital-it.ch/
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss
>




From sebastien.moretti at unil.ch  Thu Aug 12 09:48:52 2010
From: sebastien.moretti at unil.ch (=?ISO-8859-1?Q?S=E9bastien_Moretti?=)
Date: Thu, 12 Aug 2010 11:48:52 +0200
Subject: [EMBOSS] Last patched files not available on FTP
In-Reply-To: <4C63C32A.4020502@unil.ch>
References: <4C63C32A.4020502@unil.ch>
Message-ID: <4C63C384.1020003@unil.ch>

Hoops !

Sorry, cache problem in my browser.
Files are here !

> Hi
>
> last patched files are not available in
> ftp://emboss.open-bio.org/pub/EMBOSS/fixes/
>
>
> EMBOSS-6.3.1/ajax/graphics/ajgraph.c
> EMBOSS-6.3.1/ajax/ensembl/ensregistry.c
> EMBOSS-6.3.1/ajax/ajaxdb/ajseqdb.c.c
>
>
> Could you add them on the FTP server ?
>
> Do you mean ajseqdb.c.c or ajseqdb.c ?
>
> Thanks
> Regards

-- 
S?bastien Moretti
SIB Vital-IT EMBnet, Quartier Sorge - Genopode
CH-1015 Lausanne, Switzerland
Tel.: +41 (21) 692 4079/4221
http://www.vital-it.ch/ http://ch.embnet.org/ http://myhits.vital-it.ch/


From karin.lagesen at bio.uio.no  Tue Aug 24 17:43:49 2010
From: karin.lagesen at bio.uio.no (Karin Lagesen)
Date: Tue, 24 Aug 2010 19:43:49 +0200
Subject: [EMBOSS] extract translations from genbank file
Message-ID: <4C7404D5.1050100@bio.uio.no>

Hello.

I am trying to extract the protein translations from a genbank file. I 
am managing to get the proteins, but I would like to get the information 
about the translation out from the file too.

Example:

      CDS             complement(93..1919)                  		


/translation="MTLENTSPNPSQISLNLSGGIALGAYMAGVCFELVRQARKDNSP
LLIDLITGASAGAMTGAITAYYLLNREISNTEYESQNILQRAWVEKADMKDIDTVFAI 
EDYRQVLNNLFKSQNESLLSQKGIKNIANLITENTDQLKVHQPLALVMTVTNLQGLLV
/product="hypothetical protein"

I have found two programs that could solve this problem. Coderet does 
give me the protein sequences, but the fasta description lines of the 
proteins are not easily relatable back to the genbank file.

>unknown_pro_1
MTLENTSPNPSQISLNLSGGIALGAYMAGVCFELVRQARKDNSPLLIDLITGASAGAMTG
AITAYYLLNREISNTEYESQNILQRAWVEKADMKDIDTVFAIEDYRQVLNNLFKSQNESL
LSQKGIKNIANLITENTDQLKVHQPLALVMTVTNLQGLLV

Extractfeat gives me sensible description lines, but for now I have not 
been able to make it give me the protein, and not the DNA sequence.

>scaffold00002_93_1919 [CDS] Contig scaffold00002
atgaccctagaaaatacctctcccaatcctagtcaaatttccctaaatttgtcgggagga
attgccctcggagcttatatggctggggtgtgttttgaattagttagacaagccagaaaa
gacaattctcccctgttaattgatttgattaccggagcatctgctggggcgatgaccgga
....


So. Are there any other programs, or options/switches to the ones that I 
have mentioned that I should be using?


TIA,

Karin

-- 
Karin Lagesen
Post Doc
Centre of Ecological and Evolutionary Synthesis (CEES)
Department of Biology
University of Oslo
P.O. Box 1066 - Blindern
N-0316 Oslo
Norway


From john.walshaw at bbsrc.ac.uk  Tue Aug 24 19:52:09 2010
From: john.walshaw at bbsrc.ac.uk (john walshaw (JIC))
Date: Tue, 24 Aug 2010 20:52:09 +0100
Subject: [EMBOSS] Authenticated Jemboss Server and .embossrc
Message-ID: <1BBF1266FD8E1B4781FB0DC46F0E553308ED1CC27A@nbiexch1.nbi.bbsrc.ac.uk>

Hello,

should a user's own EMBOSS configuration in ~/.embossrc be picked up by an Authenticated Jemboss Server running on the same host?

I'm having problems with this - i.e. some private databases defined in ~/.embossrc work fine from the command-line. The auth Jemboss Server also seems to work fine, as far as using a Jemboss client on a PC to log in and access (with read/write) remote files on the server host is concerned. I was expecting this to mean that the logged-in user's .embossrc would also be read, but it doesn't seem to happen as for example showdb doesn't list those databases, and nothing can access any sequence records from them.

This is using EMBOSS 6.0.1/Jemboss 1.5. Can you help?

best wishes,

John Walshaw





From david.bauer at bayerhealthcare.com  Wed Aug 25 06:17:56 2010
From: david.bauer at bayerhealthcare.com (david.bauer at bayerhealthcare.com)
Date: Wed, 25 Aug 2010 08:17:56 +0200
Subject: [EMBOSS] Antwort:  extract translations from genbank file
In-Reply-To: <4C7404D5.1050100@bio.uio.no>
Message-ID: <OF6F80E7B3.D8FF3E97-ONC125778A.00221B36-C125778A.00229A5D@bayer.de>

Hi Karin,

you can pipe the output from extractfeat into transeq to get the protein 
sequence:

extractfeat  mysequence.gb -type CDS -stdout | transeq -filter

HTH,

David.

emboss-bounces at lists.open-bio.org schrieb am 24/08/2010 19:43:49:

> Extractfeat gives me sensible description lines, but for now I have not 
> been able to make it give me the protein, and not the DNA sequence.
> 
> >scaffold00002_93_1919 [CDS] Contig scaffold00002
> atgaccctagaaaatacctctcccaatcctagtcaaatttccctaaatttgtcgggagga
> attgccctcggagcttatatggctggggtgtgttttgaattagttagacaagccagaaaa
> gacaattctcccctgttaattgatttgattaccggagcatctgctggggcgatgaccgga
> ....
> 
> 
> So. Are there any other programs, or options/switches to the ones that I 

> have mentioned that I should be using?
> 
> 
> TIA,
> 
> Karin
> 
> -- 
> Karin Lagesen
> Post Doc
> Centre of Ecological and Evolutionary Synthesis (CEES)
> Department of Biology
> University of Oslo
> P.O. Box 1066 - Blindern
> N-0316 Oslo
> Norway
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss


From aengus.stewart at cancer.org.uk  Tue Aug 31 09:07:10 2010
From: aengus.stewart at cancer.org.uk (Aengus Stewart)
Date: Tue, 31 Aug 2010 10:07:10 +0100
Subject: [EMBOSS] dbxflat problem
In-Reply-To: <6967ac4e0812100700s3708c00br7dbc606e79a6529c@mail.gmail.com>
References: <6967ac4e0812100700s3708c00br7dbc606e79a6529c@mail.gmail.com>
Message-ID: <4C7CC63E.2050007@cancer.org.uk>


Hi folks,

Not sure if I am doing something wrong but I am getting an error from 6.3.1 on Redhat EL5



dbxflat -verbose -idformat swiss -directory . -filenames "*.dat" -dbname trembl -dbresource trembl 
-release - -date 29/08/10 -fields id,acc,sv,des,key,org -outfile emboss.index.log
Index a flat file database using b+tree indices

    EMBOSS An error in ajindex.c at line 702:
Maximum retries (100) reached in btreeCacheFetch for page 1069056


Actually I am getting the same error with dbiflat as well.

dbxfasta -idformat gcgidacc -directory /data/INCOMING/nrprot -filenames nrprot.fasta -dbname nrprot 
-dbresource nrprot -release "-" -date 29/08/10 -fields "acc,sv,des" -outfile emboss.index.log
Index a fasta file database using b+tree indices

    EMBOSS An error in ajindex.c at line 702:
Maximum retries (100) reached in btreeCacheFetch for page 2774040576


Aengus


-- 
-----------------------------------------------------------------------
Aengus Stewart                                 Tel: +44 (0)20 7269 3679
Head of Bioinformatics and BioStatistics
CRUK London Research Institute
Lincoln's Inn Fields, Holborn, London, WC2A 3PX, UK
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>From 1 October 2010 our registered address will be Angel Building, 407 St John Street, London, EC1V 4AD.  
 
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From ajb at ebi.ac.uk  Tue Aug 31 10:52:20 2010
From: ajb at ebi.ac.uk (ajb at ebi.ac.uk)
Date: Tue, 31 Aug 2010 11:52:20 +0100 (BST)
Subject: [EMBOSS] dbxflat problem
In-Reply-To: <4C7CC63E.2050007@cancer.org.uk>
References: <6967ac4e0812100700s3708c00br7dbc606e79a6529c@mail.gmail.com>
	<4C7CC63E.2050007@cancer.org.uk>
Message-ID: <45956.86.26.12.63.1283251940.squirrel@webmail.ebi.ac.uk>

Hi Aengus,

Are you saying that it's restricted to RHEL5 or that it's the only
platform you've tried it on.

Assuming it's not restricted to RHEL5 then first check your RES
definitions in your emboss.default (or .embossrc) to verify that
the field lengths are not set too small.

If they look OK then you'd need to post us:

  a) Your RES definitions
  b) A URL/site and specify where we can get exactly the source
     data you are trying to index. Tell us of any modifications
     made to the data.
  c) The command lines used (already given below), plus any responses
     to any further prompts.

We could then attempt to reproduce the error.

HTH

Alan



>
> Hi folks,
>
> Not sure if I am doing something wrong but I am getting an error from
> 6.3.1 on Redhat EL5
>
>
>
> dbxflat -verbose -idformat swiss -directory . -filenames "*.dat" -dbname
> trembl -dbresource trembl
> -release - -date 29/08/10 -fields id,acc,sv,des,key,org -outfile
> emboss.index.log
> Index a flat file database using b+tree indices
>
>     EMBOSS An error in ajindex.c at line 702:
> Maximum retries (100) reached in btreeCacheFetch for page 1069056
>
>
> Actually I am getting the same error with dbiflat as well.
>
> dbxfasta -idformat gcgidacc -directory /data/INCOMING/nrprot -filenames
> nrprot.fasta -dbname nrprot
> -dbresource nrprot -release "-" -date 29/08/10 -fields "acc,sv,des"
> -outfile emboss.index.log
> Index a fasta file database using b+tree indices
>
>     EMBOSS An error in ajindex.c at line 702:
> Maximum retries (100) reached in btreeCacheFetch for page 2774040576
>
>
> Aengus
>
>
> --
> -----------------------------------------------------------------------
> Aengus Stewart                                 Tel: +44 (0)20 7269 3679
> Head of Bioinformatics and BioStatistics
> CRUK London Research Institute
> Lincoln's Inn Fields, Holborn, London, WC2A 3PX, UK
> -----------------------------------------------------------------------
>
> This electronic message contains information which may be privileged and
> confidential.  The information is intended to be for the use of the
> individual(s) or entity named above. Be aware that any third party
> disclosure, distribution, copying or use of this communication, without
> prior permission, is strictly prohibited.
>
> This communication is from Cancer Research UK. Our website is at
> www.cancerresearchuk.org. We are a registered charity in England and Wales
> (1089464) and in Scotland (SC041666) and a company limited by guarantee
> registered in England and Wales under number 4325234. Our registered
> address is 61 Lincoln's Inn Fields, London WC2A 3PX. Our central telephone
> number is 020 7242 0200.
>
>>From 1 October 2010 our registered address will be Angel Building, 407 St
>> John Street, London, EC1V 4AD.
>
> This communication and any attachments contain information which is
> confidential and may also be privileged.   It is for the exclusive use of
> the intended recipient(s).  If you are not the intended recipient(s)
> please note that any form of disclosure, distribution, copying or use of
> this communication or the information in it or in any attachments is
> strictly prohibited and may be unlawful.  If you have received this
> communication in error, please notify the sender and delete the email and
> destroy any copies of it.
>
> E-mail communications cannot be guaranteed to be secure or error free, as
> information could be intercepted, corrupted, amended, lost, destroyed,
> arrive late or incomplete, or contain viruses.  We do not accept liability
> for any such matters or their consequences.  Anyone who communicates with
> us by e-mail is taken to accept the risks in doing so.
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss
>