From Richard.Casey at ColoState.EDU  Tue Nov  9 13:31:24 2010
From: Richard.Casey at ColoState.EDU (Casey,Richard)
Date: Tue, 9 Nov 2010 18:31:24 +0000
Subject: [EMBOSS] Jemboss sequence not found
Message-ID: <199D272F308D2549A861D7ABAAC5197D0AA77169@ex14.colostate.edu>

Hi,

I have Jemboss installed on Windows XP.  For any application in Jemboss, when I use Browse Files and choose a filename (full absolute path), choose Input Sequence Options and then Load Sequence Attributes, it always says "Sequence Not Found".  It doesn't matter where the file is located on drive or what the path is or what type of file.  It always says sequence not found.  Does anyone know why this is happening?  

----------------------------------
Richard


From Richard.Casey at ColoState.EDU  Tue Nov  9 13:30:36 2010
From: Richard.Casey at ColoState.EDU (Casey,Richard)
Date: Tue, 9 Nov 2010 18:30:36 +0000
Subject: [EMBOSS] Jemboss sequence not found
Message-ID: <199D272F308D2549A861D7ABAAC5197D0AA7715B@ex14.colostate.edu>

Hi,

I have Jemboss installed on Windows XP.  For any application in Jemboss, when I use Browse Files and choose a filename (full absolute path), choose Input Sequence Options and then Load Sequence Attributes, it always says "Sequence Not Found".  It doesn't matter where the file is located on drive or what the path is or what type of file.  It always says sequence not found.  Does anyone know why this is happening?  

----------------------------------
Richard



From uludag at ebi.ac.uk  Tue Nov  9 17:01:19 2010
From: uludag at ebi.ac.uk (Mahmut Uludag)
Date: Tue, 9 Nov 2010 22:01:19 -0000
Subject: [EMBOSS] Jemboss sequence not found
In-Reply-To: <199D272F308D2549A861D7ABAAC5197D0AA7715B@ex14.colostate.edu>
References: <199D272F308D2549A861D7ABAAC5197D0AA7715B@ex14.colostate.edu>
Message-ID: <1F05C1D924E34B8B9E8B7A0A561EFFB6@MedionPC>

Hi Richard,

> I have Jemboss installed on Windows XP.  For any application in Jemboss, 
> when I use Browse Files and choose a filename (full absolute path), choose 
> Input Sequence Options and then Load Sequence Attributes, it always says 
> "Sequence Not Found".  It doesn't matter where the file is located on 
> drive or what the path is or what type of file.  It always says sequence 
> not found.  Does anyone know why this is happening?

Does jemboss work otherwise if you don't select Load Sequence Attributes 
option? for example does seqret or infoseq applications return successfully 
for your input files.

It looks like I get 'Sequence Not Found' error only if I select pdf or exe 
files which are not valid sequence files.

Regards,
Mahmut
 


From biopython at maubp.freeserve.co.uk  Mon Nov 15 05:57:19 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Mon, 15 Nov 2010 10:57:19 +0000
Subject: [EMBOSS] Keep feature in union of GenBank files
Message-ID: <AANLkTimWYU+fEsRRysjbv7h7DZCGs-b+CXTXYARAVv5v@mail.gmail.com>

Hi all,

Prompted by this thread on seqanswers.com I tried using EMBOSS 6.3.1
union to merge multiple GenBank format records (in a single file) into a
single GenBank record with the concatenated sequence. This worked,
but the output file has no features:

http://seqanswers.com/forums/showthread.php?t=7812

e.g.

union -sequence many.gbk -sformat genbank -outseq merged.gbk -osformat
genbank -auto

Is support for features something that could be added to union please?

Thanks,

Peter

From biopython at maubp.freeserve.co.uk  Mon Nov 15 06:48:28 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Mon, 15 Nov 2010 11:48:28 +0000
Subject: [EMBOSS] Keep feature in union of GenBank files
In-Reply-To: <AANLkTimWYU+fEsRRysjbv7h7DZCGs-b+CXTXYARAVv5v@mail.gmail.com>
References: <AANLkTimWYU+fEsRRysjbv7h7DZCGs-b+CXTXYARAVv5v@mail.gmail.com>
Message-ID: <AANLkTi=aNSNpZF0=GchiaAz+xcwVveQ4u8L1s2zSi0yf@mail.gmail.com>

On Mon, Nov 15, 2010 at 10:57 AM, Peter <biopython at maubp.freeserve.co.uk> wrote:
> Hi all,
>
> Prompted by this thread on seqanswers.com I tried using EMBOSS 6.3.1
> union to merge multiple GenBank format records (in a single file) into a
> single GenBank record with the concatenated sequence. This worked,
> but the output file has no features:
>
> http://seqanswers.com/forums/showthread.php?t=7812
>
> e.g.
>
> union -sequence many.gbk -sformat genbank -outseq merged.gbk -osformat
> genbank -auto
>
> Is support for features something that could be added to union please?
>

Thanks to Nick Loman for the seqanswers.com thread for pointing out this
functionality is present but must be enabled explicitly with "-feature Y".

Apologies for the noise.

Peter

P.S. Why isn't this the default?

From pmr at ebi.ac.uk  Mon Nov 15 08:17:03 2010
From: pmr at ebi.ac.uk (Peter Rice)
Date: Mon, 15 Nov 2010 13:17:03 +0000
Subject: [EMBOSS] Keep feature in union of GenBank files
In-Reply-To: <AANLkTimWYU+fEsRRysjbv7h7DZCGs-b+CXTXYARAVv5v@mail.gmail.com>
References: <AANLkTimWYU+fEsRRysjbv7h7DZCGs-b+CXTXYARAVv5v@mail.gmail.com>
Message-ID: <4CE132CF.1040603@ebi.ac.uk>

On 15/11/2010 10:57, Peter Cock wrote:
> Is support for features something that could be added to union please?

Beat you to it ... there is already a -feature option

EMBOSS ignores feature information unless the application will make use 
of it, so it often has to be turned on. seqret -feature is another example.

regards,

Peter Rice

From jean-marc-cazarre at wanadoo.fr  Wed Nov 17 10:14:19 2010
From: jean-marc-cazarre at wanadoo.fr (jean-marc-cazarre at wanadoo.fr)
Date: Wed, 17 Nov 2010 16:14:19 +0100 (CET)
Subject: [EMBOSS] Question about proxy configuration
Message-ID: <22928671.171011290006859053.JavaMail.www@wwinf5a04>

Dear all,

I'm a newbie in Emboss and i have a question about proxy configuration.

The proxy of my company needs an authentication and i don't find any topic about this here or in the docs.

So my question is, is it possible to configure a proxy user/password in emboss? 

Thanks by advance for your help.

Regards

Jean-Marc



From ajb at ebi.ac.uk  Wed Nov 17 10:50:42 2010
From: ajb at ebi.ac.uk (ajb at ebi.ac.uk)
Date: Wed, 17 Nov 2010 15:50:42 -0000 (UTC)
Subject: [EMBOSS] Question about proxy configuration
In-Reply-To: <22928671.171011290006859053.JavaMail.www@wwinf5a04>
References: <22928671.171011290006859053.JavaMail.www@wwinf5a04>
Message-ID: <47481.86.26.12.63.1290009042.squirrel@webmail.ebi.ac.uk>

Hello Jean-Marc,

It is not possible to configure a proxy user/password  in the current
stable release of EMBOSS. It will, however, be possible to use
'Basic' (not 'Digest' nor 'NTLM') proxy authentication in the next
release. It is also currently possible to do so using the developers' CVS
version of EMBOSS.

Authentication is specified by extending the current syntax of the
EMBOSS_PROXY environment variable (or by using "set PROXY" in
emboss.defaults or .embossrc)

The current syntax is:

  set PROXY "host:port"

The new syntax is:

  set PROXY "host:port Basic username:password"

with the 'Basic username:password' part being optional.

Alan


> Dear all,
>
> I'm a newbie in Emboss and i have a question about proxy configuration.
>
> The proxy of my company needs an authentication and i don't find any topic
> about this here or in the docs.
>
> So my question is, is it possible to configure a proxy user/password in
> emboss?
>
> Thanks by advance for your help.
>
> Regards
>
> Jean-Marc
>
>
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss
>



From Richard.Casey at ColoState.EDU  Tue Nov  9 18:31:24 2010
From: Richard.Casey at ColoState.EDU (Casey,Richard)
Date: Tue, 9 Nov 2010 18:31:24 +0000
Subject: [EMBOSS] Jemboss sequence not found
Message-ID: <199D272F308D2549A861D7ABAAC5197D0AA77169@ex14.colostate.edu>

Hi,

I have Jemboss installed on Windows XP.  For any application in Jemboss, when I use Browse Files and choose a filename (full absolute path), choose Input Sequence Options and then Load Sequence Attributes, it always says "Sequence Not Found".  It doesn't matter where the file is located on drive or what the path is or what type of file.  It always says sequence not found.  Does anyone know why this is happening?  

----------------------------------
Richard



From Richard.Casey at ColoState.EDU  Tue Nov  9 18:30:36 2010
From: Richard.Casey at ColoState.EDU (Casey,Richard)
Date: Tue, 9 Nov 2010 18:30:36 +0000
Subject: [EMBOSS] Jemboss sequence not found
Message-ID: <199D272F308D2549A861D7ABAAC5197D0AA7715B@ex14.colostate.edu>

Hi,

I have Jemboss installed on Windows XP.  For any application in Jemboss, when I use Browse Files and choose a filename (full absolute path), choose Input Sequence Options and then Load Sequence Attributes, it always says "Sequence Not Found".  It doesn't matter where the file is located on drive or what the path is or what type of file.  It always says sequence not found.  Does anyone know why this is happening?  

----------------------------------
Richard




From uludag at ebi.ac.uk  Tue Nov  9 22:01:19 2010
From: uludag at ebi.ac.uk (Mahmut Uludag)
Date: Tue, 9 Nov 2010 22:01:19 -0000
Subject: [EMBOSS] Jemboss sequence not found
In-Reply-To: <199D272F308D2549A861D7ABAAC5197D0AA7715B@ex14.colostate.edu>
References: <199D272F308D2549A861D7ABAAC5197D0AA7715B@ex14.colostate.edu>
Message-ID: <1F05C1D924E34B8B9E8B7A0A561EFFB6@MedionPC>

Hi Richard,

> I have Jemboss installed on Windows XP.  For any application in Jemboss, 
> when I use Browse Files and choose a filename (full absolute path), choose 
> Input Sequence Options and then Load Sequence Attributes, it always says 
> "Sequence Not Found".  It doesn't matter where the file is located on 
> drive or what the path is or what type of file.  It always says sequence 
> not found.  Does anyone know why this is happening?

Does jemboss work otherwise if you don't select Load Sequence Attributes 
option? for example does seqret or infoseq applications return successfully 
for your input files.

It looks like I get 'Sequence Not Found' error only if I select pdf or exe 
files which are not valid sequence files.

Regards,
Mahmut
 



From biopython at maubp.freeserve.co.uk  Mon Nov 15 10:57:19 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Mon, 15 Nov 2010 10:57:19 +0000
Subject: [EMBOSS] Keep feature in union of GenBank files
Message-ID: <AANLkTimWYU+fEsRRysjbv7h7DZCGs-b+CXTXYARAVv5v@mail.gmail.com>

Hi all,

Prompted by this thread on seqanswers.com I tried using EMBOSS 6.3.1
union to merge multiple GenBank format records (in a single file) into a
single GenBank record with the concatenated sequence. This worked,
but the output file has no features:

http://seqanswers.com/forums/showthread.php?t=7812

e.g.

union -sequence many.gbk -sformat genbank -outseq merged.gbk -osformat
genbank -auto

Is support for features something that could be added to union please?

Thanks,

Peter


From biopython at maubp.freeserve.co.uk  Mon Nov 15 11:48:28 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Mon, 15 Nov 2010 11:48:28 +0000
Subject: [EMBOSS] Keep feature in union of GenBank files
In-Reply-To: <AANLkTimWYU+fEsRRysjbv7h7DZCGs-b+CXTXYARAVv5v@mail.gmail.com>
References: <AANLkTimWYU+fEsRRysjbv7h7DZCGs-b+CXTXYARAVv5v@mail.gmail.com>
Message-ID: <AANLkTi=aNSNpZF0=GchiaAz+xcwVveQ4u8L1s2zSi0yf@mail.gmail.com>

On Mon, Nov 15, 2010 at 10:57 AM, Peter <biopython at maubp.freeserve.co.uk> wrote:
> Hi all,
>
> Prompted by this thread on seqanswers.com I tried using EMBOSS 6.3.1
> union to merge multiple GenBank format records (in a single file) into a
> single GenBank record with the concatenated sequence. This worked,
> but the output file has no features:
>
> http://seqanswers.com/forums/showthread.php?t=7812
>
> e.g.
>
> union -sequence many.gbk -sformat genbank -outseq merged.gbk -osformat
> genbank -auto
>
> Is support for features something that could be added to union please?
>

Thanks to Nick Loman for the seqanswers.com thread for pointing out this
functionality is present but must be enabled explicitly with "-feature Y".

Apologies for the noise.

Peter

P.S. Why isn't this the default?


From pmr at ebi.ac.uk  Mon Nov 15 13:17:03 2010
From: pmr at ebi.ac.uk (Peter Rice)
Date: Mon, 15 Nov 2010 13:17:03 +0000
Subject: [EMBOSS] Keep feature in union of GenBank files
In-Reply-To: <AANLkTimWYU+fEsRRysjbv7h7DZCGs-b+CXTXYARAVv5v@mail.gmail.com>
References: <AANLkTimWYU+fEsRRysjbv7h7DZCGs-b+CXTXYARAVv5v@mail.gmail.com>
Message-ID: <4CE132CF.1040603@ebi.ac.uk>

On 15/11/2010 10:57, Peter Cock wrote:
> Is support for features something that could be added to union please?

Beat you to it ... there is already a -feature option

EMBOSS ignores feature information unless the application will make use 
of it, so it often has to be turned on. seqret -feature is another example.

regards,

Peter Rice


From jean-marc-cazarre at wanadoo.fr  Wed Nov 17 15:14:19 2010
From: jean-marc-cazarre at wanadoo.fr (jean-marc-cazarre at wanadoo.fr)
Date: Wed, 17 Nov 2010 16:14:19 +0100 (CET)
Subject: [EMBOSS] Question about proxy configuration
Message-ID: <22928671.171011290006859053.JavaMail.www@wwinf5a04>

Dear all,

I'm a newbie in Emboss and i have a question about proxy configuration.

The proxy of my company needs an authentication and i don't find any topic about this here or in the docs.

So my question is, is it possible to configure a proxy user/password in emboss? 

Thanks by advance for your help.

Regards

Jean-Marc




From ajb at ebi.ac.uk  Wed Nov 17 15:50:42 2010
From: ajb at ebi.ac.uk (ajb at ebi.ac.uk)
Date: Wed, 17 Nov 2010 15:50:42 -0000 (UTC)
Subject: [EMBOSS] Question about proxy configuration
In-Reply-To: <22928671.171011290006859053.JavaMail.www@wwinf5a04>
References: <22928671.171011290006859053.JavaMail.www@wwinf5a04>
Message-ID: <47481.86.26.12.63.1290009042.squirrel@webmail.ebi.ac.uk>

Hello Jean-Marc,

It is not possible to configure a proxy user/password  in the current
stable release of EMBOSS. It will, however, be possible to use
'Basic' (not 'Digest' nor 'NTLM') proxy authentication in the next
release. It is also currently possible to do so using the developers' CVS
version of EMBOSS.

Authentication is specified by extending the current syntax of the
EMBOSS_PROXY environment variable (or by using "set PROXY" in
emboss.defaults or .embossrc)

The current syntax is:

  set PROXY "host:port"

The new syntax is:

  set PROXY "host:port Basic username:password"

with the 'Basic username:password' part being optional.

Alan


> Dear all,
>
> I'm a newbie in Emboss and i have a question about proxy configuration.
>
> The proxy of my company needs an authentication and i don't find any topic
> about this here or in the docs.
>
> So my question is, is it possible to configure a proxy user/password in
> emboss?
>
> Thanks by advance for your help.
>
> Regards
>
> Jean-Marc
>
>
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss
>