load annotations or future file

nail · 1 July 2019 19:07

I just would like to load annotations or future file with *.json. Every single time, it gives error loading file. Also, I showed [https://www.ebi.ac.uk/pdbe/pdbe-kb](https://www.ebi.ac.uk/pdbe/pdbe-kb`) as a resource to load the sequence future is das settings. But it doesn’t work. pls help me with this problem

Best

g_m_carstairs · 2 July 2019 08:48

Hello Nail,

I am sorry to hear you are having problems.

An annotation or features file should be plain text format, not JSON. Please see the help pages in the application or at

http://www.jalview.org/help/html/features/annotationsFormat.html

http://www.jalview.org/help/html/features/featuresFormat.html

The DAS service registry was unfortunately discontinued in 2015 (see https://www.dasregistry.org/), and DAS options will be removed in the forthcoming release of Jalview.

However you can still fetch annotation from PDB, Uniprot and other EBI databases using the menu option “Web Service | Fetch DB References”.

I hope this helps. If you are still having problems, please let us know the version of Jalview you are running, any error messages seen (“Tools | Show Java Console”), and if possible email me the file(s) that fail to load.

···

Best regards,

Mungo

Mungo Carstairs
Jalview Computational Scientist

The Barton Group
Division of Computational Biology

School of Life Sciences

University of Dundee, Dundee, Scotland, UK

www.jalview.org

www.compbio.dundee.ac.uk
g.m.carstairs@dundee.ac.uk

We’re Scottish University of the Year again!
The Times / Sunday Times Good University Guide 2016 and 2017

From: jalview-discuss-bounces@jalview.org jalview-discuss-bounces@jalview.org on behalf of Nail Besli beslinail@gmail.com
Sent: 01 July 2019 20:07:46
To: jalview-discuss@jalview.org
Subject: [Jalview-discuss] load annotations or future file

I just would like to load annotations or future file with *.json. Every single time, it gives error loading file. Also, I showed [https://www.ebi.ac.uk/pdbe/pdbe-kb](https://www.ebi.ac.uk/pdbe/pdbe-kb`) as a resource to load the sequence future is das settings. But it doesn’t work. pls help me with this problem

Best

The University of Dundee is a registered Scottish Charity, No: SC015096

j_procter · 2 July 2019 09:51

Hi Nail.

Annotations from the PDBe-kb would be useful to others - we'd be happy
to help you if you'd like to write a parser so Jalview could
automatically import PDBe-kb annotation !

Jim.

···

On 02/07/2019 09:48, Mungo Carstairs (Staff) wrote:

------------------------------------------------------------------------
*From:* jalview-discuss-bounces@jalview.org
<jalview-discuss-bounces@jalview.org> on behalf of Nail Besli
<beslinail@gmail.com>
*Sent:* 01 July 2019 20:07:46
*To:* jalview-discuss@jalview.org
*Subject:* [Jalview-discuss] load annotations or future file
I just would like to load annotations or future file with *.json.
Every single time, it gives error loading file. Also, I showed
`https://www.ebi.ac.uk/pdbe/pdbe-kb\` as a resource to load the sequence
future is das settings. But it doesn't work. pls help me with this problem

Best

The University of Dundee is a registered Scottish Charity, No: SC015096

_______________________________________________
Jalview-discuss mailing list
Jalview-discuss@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss

--
-------------------------------------------------------------------
Dr JB Procter, Jalview Coordinator, The Barton Group
Division of Computational Biology, School of Life Sciences
University of Dundee, Dundee DD1 5EH, UK.
+44 1382 388734 | www.jalview.org | www.compbio.dundee.ac.uk

The University of Dundee is a registered Scottish Charity, No: SC015096

geoff.barton · 2 July 2019 10:18

Hi Jim (not to Nail),

Of course we are part of the PDBe-KB project as collaborators as well,
well STuart is...

Geoff.

···

On 02/07/2019 10:51, James Procter (Staff) wrote:

Hi Nail.

Annotations from the PDBe-kb would be useful to others - we'd be happy
to help you if you'd like to write a parser so Jalview could
automatically import PDBe-kb annotation !

Jim.

On 02/07/2019 09:48, Mungo Carstairs (Staff) wrote:

------------------------------------------------------------------------
*From:* jalview-discuss-bounces@jalview.org
<jalview-discuss-bounces@jalview.org> on behalf of Nail Besli
<beslinail@gmail.com>
*Sent:* 01 July 2019 20:07:46
*To:* jalview-discuss@jalview.org
*Subject:* [Jalview-discuss] load annotations or future file
I just would like to load annotations or future file with *.json.
Every single time, it gives error loading file. Also, I showed
`https://www.ebi.ac.uk/pdbe/pdbe-kb\` as a resource to load the sequence
future is das settings. But it doesn't work. pls help me with this problem

Best

The University of Dundee is a registered Scottish Charity, No: SC015096

_______________________________________________
Jalview-discuss mailing list
Jalview-discuss@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss

--
-------------------------------------------------------------------
Dr JB Procter, Jalview Coordinator, The Barton Group
Division of Computational Biology, School of Life Sciences
University of Dundee, Dundee DD1 5EH, UK.
+44 1382 388734 | www.jalview.org | www.compbio.dundee.ac.uk

The University of Dundee is a registered Scottish Charity, No: SC015096
_______________________________________________
Jalview-discuss mailing list
Jalview-discuss@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss

The University of Dundee is registered Scottish charity: No.SC015096

The University of Dundee is a registered Scottish Charity, No: SC015096

geoff.barton · 2 July 2019 10:21

Dear All,

Was trying to minimise expectations there, but happy for the list to
know that we are collaborators on PDBe-KB and so will in time be making
better access to the annotations there from within Jalview.

Of course, if anyone would like to help with parsers that would be
great. Jalview is an open source project and we welcome collaboration
on enhancing its functions.

Geoff.

···

On 02/07/2019 11:18, Geoff Barton wrote:

Hi Jim (not to Nail),

Of course we are part of the PDBe-KB project as collaborators as well,
well STuart is...

Geoff.

On 02/07/2019 10:51, James Procter (Staff) wrote:

Hi Nail.

Annotations from the PDBe-kb would be useful to others - we'd be happy
to help you if you'd like to write a parser so Jalview could
automatically import PDBe-kb annotation !

Jim.

On 02/07/2019 09:48, Mungo Carstairs (Staff) wrote:

------------------------------------------------------------------------

*From:* jalview-discuss-bounces@jalview.org
<jalview-discuss-bounces@jalview.org> on behalf of Nail Besli
<beslinail@gmail.com>
*Sent:* 01 July 2019 20:07:46
*To:* jalview-discuss@jalview.org
*Subject:* [Jalview-discuss] load annotations or future file
I just would like to load annotations or future file with *.json.
Every single time, it gives error loading file. Also, I showed
`https://www.ebi.ac.uk/pdbe/pdbe-kb\` as a resource to load the sequence
future is das settings. But it doesn't work. pls help me with this
problem

Best

The University of Dundee is a registered Scottish Charity, No: SC015096

_______________________________________________
Jalview-discuss mailing list
Jalview-discuss@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss

--
-------------------------------------------------------------------
Dr JB Procter, Jalview Coordinator, The Barton Group
Division of Computational Biology, School of Life Sciences
University of Dundee, Dundee DD1 5EH, UK.
+44 1382 388734 | www.jalview.org | www.compbio.dundee.ac.uk

The University of Dundee is a registered Scottish Charity, No: SC015096
_______________________________________________
Jalview-discuss mailing list
Jalview-discuss@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss

The University of Dundee is registered Scottish charity: No.SC015096

The University of Dundee is a registered Scottish Charity, No: SC015096

jalviewbugreporter · 2 July 2019 11:23

Thanks Geoff.

···

On 02/07/2019 11:21, Geoff Barton wrote:

Was trying to minimise expectations there, but happy for the list to
know that we are collaborators on PDBe-KB and so will in time be making
better access to the annotations there from within Jalview.

Of course, if anyone would like to help with parsers that would be
great. Jalview is an open source project and we welcome collaboration
on enhancing its functions.

I'm very keen that we define a simple API that allows anyone to create annotation retrieval plugins provided as a groovy script or java/java2script fragment. PDBe-KB would be a good use case for this.

Jim.

g_m_carstairs · 3 July 2019 07:32

Hello Nail,

You need to reformat the columns of your csv file to match the Jalview features file format (as described at

···

Mungo Carstairs
Jalview Computational Scientist

The Barton Group
Division of Computational Biology

School of Life Sciences

University of Dundee, Dundee, Scotland, UK

www.jalview.org

www.compbio.dundee.ac.uk
g.m.carstairs@dundee.ac.uk

We’re Scottish University of the Year again!
The Times / Sunday Times Good University Guide 2016 and 2017

From: Nail Besli beslinail@gmail.com
Sent: 02 July 2019 13:37:50
To: Mungo Carstairs (Staff)
Subject: Re: [Jalview-discuss] load annotations or future file

Thank you all. I really appreciate. My spesific problem is that attached files are not able to load features/annotations in section of File in JALview 2.10.5. How can I cope with it. Should I modify these files format?

On Tue, Jul 2, 2019 at 11:48 AM Mungo Carstairs (Staff) <g.m.carstairs@dundee.ac.uk> wrote:

Hello Nail,

I am sorry to hear you are having problems.

An annotation or features file should be plain text format, not JSON. Please see the help pages in the application or at

http://www.jalview.org/help/html/features/annotationsFormat.html

http://www.jalview.org/help/html/features/featuresFormat.html

The DAS service registry was unfortunately discontinued in 2015 (see https://www.dasregistry.org/), and DAS options will be removed in the forthcoming release of Jalview.

However you can still fetch annotation from PDB, Uniprot and other EBI databases using the menu option “Web Service | Fetch DB References”.

I hope this helps. If you are still having problems, please let us know the version of Jalview you are running, any error messages seen (“Tools | Show Java Console”), and if possible email me the file(s) that fail to load.

Best regards,

Mungo

Mungo Carstairs
Jalview Computational Scientist

The Barton Group
Division of Computational Biology

School of Life Sciences

University of Dundee, Dundee, Scotland, UK

www.jalview.org

www.compbio.dundee.ac.uk
g.m.carstairs@dundee.ac.uk

We’re Scottish University of the Year again!
The Times / Sunday Times Good University Guide 2016 and 2017

From: jalview-discuss-bounces@jalview.org <jalview-discuss-bounces@jalview.org> on behalf of Nail Besli <beslinail@gmail.com>
Sent: 01 July 2019 20:07:46
To: jalview-discuss@jalview.org
Subject: [Jalview-discuss] load annotations or future file

I just would like to load annotations or future file with *.json. Every single time, it gives error loading file. Also, I showed [https://www.ebi.ac.uk/pdbe/pdbe-kb](https://www.ebi.ac.uk/pdbe/pdbe-kb) as a resource to load the sequence future is das settings. But it doesn’t work. pls help me with this problem

Best

The University of Dundee is a registered Scottish Charity, No: SC015096

The University of Dundee is a registered Scottish Charity, No: SC015096

g_m_carstairs · 3 July 2019 07:46

Hello Nail,

You need to reorder the columns of your csv file to match the Jalview features file format (as described at http://www.jalview.org/help/html/features/featuresFormat.html).

If you are on Unix/OSX and have the awk command available, you could try this:

awk -F’,’ -v OFS=‘\t’ ‘{ print $2,$1,“-1”,$4,$5,$3 }’ P11169-coverage.csv > features.txt

This writes out columns 2,1,4,5,3 of the csv to output file features.txt.

-F’,’ specifies comma as the field separator in the input file
OFS=‘\t’ specifies tab as the field separator in the output file

I was able to load the output as a features file in Jalview.

Adapt as required!

Reformatting the JSON file would be rather more work, or need a parser to be coded.

Best regards,

Mungo

p.s. ignore last incomplete email. I shouldn’t try to email from a moving bus!

The University of Dundee is a registered Scottish Charity, No: SC015096

···

Mungo Carstairs
Jalview Computational Scientist

The Barton Group
Division of Computational Biology

School of Life Sciences

University of Dundee, Dundee, Scotland, UK

www.jalview.org

www.compbio.dundee.ac.uk
g.m.carstairs@dundee.ac.uk

We’re Scottish University of the Year again!
The Times / Sunday Times Good University Guide 2016 and 2017

From: Mungo Carstairs (Staff)
Sent: 03 July 2019 08:32:00
To: Nail Besli; jalview-discuss@jalview.org
Subject: Re: [Jalview-discuss] load annotations or future file

Hello Nail,

You need to reformat the columns of your csv file to match the Jalview features file format (as described at

Mungo Carstairs
Jalview Computational Scientist

The Barton Group
Division of Computational Biology

School of Life Sciences

University of Dundee, Dundee, Scotland, UK

www.jalview.org

www.compbio.dundee.ac.uk
g.m.carstairs@dundee.ac.uk

We’re Scottish University of the Year again!
The Times / Sunday Times Good University Guide 2016 and 2017

From: Nail Besli beslinail@gmail.com
Sent: 02 July 2019 13:37:50
To: Mungo Carstairs (Staff)
Subject: Re: [Jalview-discuss] load annotations or future file

Thank you all. I really appreciate. My spesific problem is that attached files are not able to load features/annotations in section of File in JALview 2.10.5. How can I cope with it. Should I modify these files format?

On Tue, Jul 2, 2019 at 11:48 AM Mungo Carstairs (Staff) <g.m.carstairs@dundee.ac.uk> wrote:

Hello Nail,

I am sorry to hear you are having problems.

An annotation or features file should be plain text format, not JSON. Please see the help pages in the application or at

http://www.jalview.org/help/html/features/annotationsFormat.html

http://www.jalview.org/help/html/features/featuresFormat.html

The DAS service registry was unfortunately discontinued in 2015 (see https://www.dasregistry.org/), and DAS options will be removed in the forthcoming release of Jalview.

However you can still fetch annotation from PDB, Uniprot and other EBI databases using the menu option “Web Service | Fetch DB References”.

I hope this helps. If you are still having problems, please let us know the version of Jalview you are running, any error messages seen (“Tools | Show Java Console”), and if possible email me the file(s) that fail to load.

Best regards,

Mungo

Mungo Carstairs
Jalview Computational Scientist

The Barton Group
Division of Computational Biology

School of Life Sciences

University of Dundee, Dundee, Scotland, UK

www.jalview.org

www.compbio.dundee.ac.uk
g.m.carstairs@dundee.ac.uk

We’re Scottish University of the Year again!
The Times / Sunday Times Good University Guide 2016 and 2017

From: jalview-discuss-bounces@jalview.org <jalview-discuss-bounces@jalview.org> on behalf of Nail Besli <beslinail@gmail.com>
Sent: 01 July 2019 20:07:46
To: jalview-discuss@jalview.org
Subject: [Jalview-discuss] load annotations or future file

I just would like to load annotations or future file with *.json. Every single time, it gives error loading file. Also, I showed [https://www.ebi.ac.uk/pdbe/pdbe-kb](https://www.ebi.ac.uk/pdbe/pdbe-kb) as a resource to load the sequence future is das settings. But it doesn’t work. pls help me with this problem

Best

The University of Dundee is a registered Scottish Charity, No: SC015096

g_m_carstairs · 24 March 2020 12:17

Hi Nail,

I’m just copying the question to the discussion list so it is visible to the whole team / community, so the best person can get back to you. Please bear with us!

Best regards,

mungo

···

Mungo Carstairs
Jalview Computational Scientist

The Barton Group
Division of Computational Biology

School of Life Sciences

University of Dundee, Dundee, Scotland, UK

www.jalview.org

www.compbio.dundee.ac.uk
g.m.carstairs@dundee.ac.uk

We’re Scottish University of the Year again!
The Times / Sunday Times Good University Guide 2016 and 2017

From: Nail Besli beslinail@gmail.com
Sent: 24 March 2020 12:12
To: Mungo Carstairs (Staff) g.m.carstairs@dundee.ac.uk
Subject: Re: [Jalview-discuss] load annotations or future file

Hi,
I would like to align with three protein sequences to detect the conserved domains using CATH. How can I do it?

Nail

On Tue, Jul 2, 2019 at 11:48 AM Mungo Carstairs (Staff) <g.m.carstairs@dundee.ac.uk> wrote:

Hello Nail,

I am sorry to hear you are having problems.

An annotation or features file should be plain text format, not JSON. Please see the help pages in the application or at

http://www.jalview.org/help/html/features/annotationsFormat.html

http://www.jalview.org/help/html/features/featuresFormat.html

The DAS service registry was unfortunately discontinued in 2015 (see https://www.dasregistry.org/), and DAS options will be removed in the forthcoming release of Jalview.

However you can still fetch annotation from PDB, Uniprot and other EBI databases using the menu option “Web Service | Fetch DB References”.

I hope this helps. If you are still having problems, please let us know the version of Jalview you are running, any error messages seen (“Tools | Show Java Console”), and if possible email me the file(s) that fail to load.

Best regards,

Mungo

Mungo Carstairs
Jalview Computational Scientist

The Barton Group
Division of Computational Biology

School of Life Sciences

University of Dundee, Dundee, Scotland, UK

www.jalview.org

www.compbio.dundee.ac.uk
g.m.carstairs@dundee.ac.uk

We’re Scottish University of the Year again!
The Times / Sunday Times Good University Guide 2016 and 2017

From: jalview-discuss-bounces@jalview.org <jalview-discuss-bounces@jalview.org> on behalf of Nail Besli <beslinail@gmail.com>
Sent: 01 July 2019 20:07:46
To: jalview-discuss@jalview.org
Subject: [Jalview-discuss] load annotations or future file

I just would like to load annotations or future file with *.json. Every single time, it gives error loading file. Also, I showed [https://www.ebi.ac.uk/pdbe/pdbe-kb](https://www.ebi.ac.uk/pdbe/pdbe-kb) as a resource to load the sequence future is das settings. But it doesn’t work. pls help me with this problem

Best

The University of Dundee is a registered Scottish Charity, No: SC015096

The University of Dundee is a registered Scottish Charity, No: SC015096