Problem with sequence features file

Hello,

I have an assembly done with Clustal Omega web portal (.clustal_num file) that I imported into Jalview v. 2.11.0. Using the instructions here (http://www.jalview.org/help/html/features/featuresFormat.html) I am trying to import features into the alignment and have run into problems. Nothing is imported regardless of how I try and load the features (either drag and drop on alignment or File → Load Features/Annotations) or if I have the GFF3 section in my file. I also tried converting my clustal_num file to a .aln file and that did not solve the issue.

I have attached my Sequences Features File here in case that’s useful. Any assistance in getting the features imported would be greatly appreciated!

Thanks,

Samantha

Samantha Atkinson, PhD

Bioinformatics Analyst III

Center for Microbiome Research

Microbiology & Immunology

Medical College of Wisconsin

8701 Watertown Plank

Milwaukee, WI 53226

test_seq_features.txt (251 Bytes)

Hi Samantha,

Thanks for getting in touch, we are here to help!

I was able to load your features file on to sequences.

I added this dummy ‘sequence data’ into Jalview (File | Input alignment | from textbox):

m_macrosporus_hw_1
GLIFQWMLRSTGLIFQWMLRSTGLIFQWMLRSTGLIFQWMLRSTGLIFQWMLRSTGLIFQWMLRST
m_xanthus
GLIFQWMLRSTGLIFQWMLRSTGLIFQWMLRSTGLIFQWMLRSTGLIFQWMLRSTGLIFQWMLRST
m_flavescens
GLIFQWMLRSTGLIFQWMLRSTGLIFQWMLRSTGLIFQWMLRSTGLIFQWMLRSTGLIFQWMLRST

and the features were added ok.

Do your sequence names in Jalview exactly match the feature file?

If you open the Java Console (from the Tools menu) and try again, is any error message logged in the console?

While you are there, please copy out the Java and operating system information just in case they are relevant (though I’m guessing probably not).

The second line of your features file is 6 tab characters - but this doesn’t seem to make it fail for me.

Maybe also try replacing this with

STARTGROUPTEST

and adding

ENDGROUPTEST

after the Jalview formatted features.

This just makes it clearer in the ‘Feature Settings’ panel which features are in which group.

But your data assigns the ‘null group’ which is also valid.

Thanks,

Mungo

p.s. check out our Twitter feed from ISBM Basel at http://www.jalview.org/ and see if you spot the magician from Minnesota!

···

Email signature

University of Dundee shield logo

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

University of Dundee FacebookUniversity of Dundee TwitterUniversity of Dundee LinkedInUniversity of Dundee YouTubeUniversity of Dundee InstagramUniversity of Dundee Snapchat
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 Atkinson, Samantha saatkinson@mcw.edu
Sent: 24 July 2019 16:13:01
To: jalview-discuss@jalview.org jalview-discuss@jalview.org
Subject: [Jalview-discuss] Problem with sequence features file

Hello,

I have an assembly done with Clustal Omega web portal (.clustal_num file) that I imported into Jalview v. 2.11.0. Using the instructions here (http://www.jalview.org/help/html/features/featuresFormat.html) I am trying to import features into the alignment and have run into problems. Nothing is imported regardless of how I try and load the features (either drag and drop on alignment or File → Load Features/Annotations) or if I have the GFF3 section in my file. I also tried converting my clustal_num file to a .aln file and that did not solve the issue.

I have attached my Sequences Features File here in case that’s useful. Any assistance in getting the features imported would be greatly appreciated!

Thanks,

Samantha

Samantha Atkinson, PhD

Bioinformatics Analyst III

Center for Microbiome Research

Microbiology & Immunology

Medical College of Wisconsin

8701 Watertown Plank

Milwaukee, WI 53226

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

Hi Mungo,

Thanks for your quick response, your suggested changes worked! I had changed the names of sequences in Jalview (right click → sequence name → edit Name/Description) to make them more readable and used the shortened names in the features file (matching the sequence description). When I added the STARTGROUP and ENDGROUP lines as you suggested (and copied and pasted the full unchanged names) it worked!

Thanks for your help!

Samantha

···

From: “Mungo Carstairs (Staff)” g.m.carstairs@dundee.ac.uk
Date: Wednesday, July 24, 2019 at 10:53 AM
To: “Atkinson, Samantha” saatkinson@mcw.edu, “jalview-discuss@jalview.orgjalview-discuss@jalview.org
Subject: Re: Problem with sequence features file

ATTENTION: This email originated from a sender outside of MCW. Use caution when clicking on links or opening attachments.


Hi Samantha,

Thanks for getting in touch, we are here to help!

I was able to load your features file on to sequences.

I added this dummy ‘sequence data’ into Jalview (File | Input alignment | from textbox):

m_macrosporus_hw_1

GLIFQWMLRSTGLIFQWMLRSTGLIFQWMLRSTGLIFQWMLRSTGLIFQWMLRSTGLIFQWMLRST

m_xanthus

GLIFQWMLRSTGLIFQWMLRSTGLIFQWMLRSTGLIFQWMLRSTGLIFQWMLRSTGLIFQWMLRST

m_flavescens

GLIFQWMLRSTGLIFQWMLRSTGLIFQWMLRSTGLIFQWMLRSTGLIFQWMLRSTGLIFQWMLRST

and the features were added ok.

Do your sequence names in Jalview exactly match the feature file?

If you open the Java Console (from the Tools menu) and try again, is any error message logged in the console?

While you are there, please copy out the Java and operating system information just in case they are relevant (though I’m guessing probably not).

The second line of your features file is 6 tab characters - but this doesn’t seem to make it fail for me.

Maybe also try replacing this with

STARTGROUPTEST

and adding

ENDGROUPTEST

after the Jalview formatted features.

This just makes it clearer in the ‘Feature Settings’ panel which features are in which group.

But your data assigns the ‘null group’ which is also valid.

Thanks,

Mungo

p.s. check out our Twitter feed from ISBM Basel at http://www.jalview.org/ and see if you spot the magician from Minnesota!

Email signature

University of Dundee shield logo

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

University of Dundee FacebookUniversity of Dundee TwitterUniversity of Dundee LinkedInUniversity of Dundee YouTubeUniversity of Dundee InstagramUniversity of Dundee Snapchat

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 Atkinson, Samantha saatkinson@mcw.edu
Sent: 24 July 2019 16:13:01
To: jalview-discuss@jalview.org jalview-discuss@jalview.org
Subject: [Jalview-discuss] Problem with sequence features file

Hello,

I have an assembly done with Clustal Omega web portal (.clustal_num file) that I imported into Jalview v. 2.11.0. Using the instructions here (http://www.jalview.org/help/html/features/featuresFormat.html) I am trying to import features into the alignment and have run into problems. Nothing is imported regardless of how I try and load the features (either drag and drop on alignment or File → Load Features/Annotations) or if I have the GFF3 section in my file. I also tried converting my clustal_num file to a .aln file and that did not solve the issue.

I have attached my Sequences Features File here in case that’s useful. Any assistance in getting the features imported would be greatly appreciated!

Thanks,

Samantha

Samantha Atkinson, PhD

Bioinformatics Analyst III

Center for Microbiome Research

Microbiology & Immunology

Medical College of Wisconsin

8701 Watertown Plank

Milwaukee, WI 53226

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

Hi Samantha,

Glad that’s resolved. It may also be partly a bug on our side.

When you change the name of a displayed / aligned / gapped sequence, the name of the underlying ungapped data sequence is not changed, and this may be involved in the features file failing to match up the sequences. I’ll check whether we have work to do on that. Thanks for drawing it to our attention!

Best regards,

Mungo

···

Email signature

University of Dundee shield logo

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

University of Dundee FacebookUniversity of Dundee TwitterUniversity of Dundee LinkedInUniversity of Dundee YouTubeUniversity of Dundee InstagramUniversity of Dundee Snapchat
We’re Scottish University of the Year again!
The Times / Sunday Times Good University Guide 2016 and 2017


From: Atkinson, Samantha saatkinson@mcw.edu
Sent: 24 July 2019 17:29:50
To: Mungo Carstairs (Staff) g.m.carstairs@dundee.ac.uk; jalview-discuss@jalview.org jalview-discuss@jalview.org
Subject: Re: Problem with sequence features file

Hi Mungo,

Thanks for your quick response, your suggested changes worked! I had changed the names of sequences in Jalview (right click → sequence name → edit Name/Description) to make them more readable and used the shortened names in the features file (matching the sequence description). When I added the STARTGROUP and ENDGROUP lines as you suggested (and copied and pasted the full unchanged names) it worked!

Thanks for your help!

Samantha

From: “Mungo Carstairs (Staff)” g.m.carstairs@dundee.ac.uk
Date: Wednesday, July 24, 2019 at 10:53 AM
To: “Atkinson, Samantha” saatkinson@mcw.edu, “jalview-discuss@jalview.orgjalview-discuss@jalview.org
Subject: Re: Problem with sequence features file

ATTENTION: This email originated from a sender outside of MCW. Use caution when clicking on links or opening attachments.

Hi Samantha,

Thanks for getting in touch, we are here to help!

I was able to load your features file on to sequences.

I added this dummy ‘sequence data’ into Jalview (File | Input alignment | from textbox):

m_macrosporus_hw_1

GLIFQWMLRSTGLIFQWMLRSTGLIFQWMLRSTGLIFQWMLRSTGLIFQWMLRSTGLIFQWMLRST

m_xanthus

GLIFQWMLRSTGLIFQWMLRSTGLIFQWMLRSTGLIFQWMLRSTGLIFQWMLRSTGLIFQWMLRST

m_flavescens

GLIFQWMLRSTGLIFQWMLRSTGLIFQWMLRSTGLIFQWMLRSTGLIFQWMLRSTGLIFQWMLRST

and the features were added ok.

Do your sequence names in Jalview exactly match the feature file?

If you open the Java Console (from the Tools menu) and try again, is any error message logged in the console?

While you are there, please copy out the Java and operating system information just in case they are relevant (though I’m guessing probably not).

The second line of your features file is 6 tab characters - but this doesn’t seem to make it fail for me.

Maybe also try replacing this with

STARTGROUPTEST

and adding

ENDGROUPTEST

after the Jalview formatted features.

This just makes it clearer in the ‘Feature Settings’ panel which features are in which group.

But your data assigns the ‘null group’ which is also valid.

Thanks,

Mungo

p.s. check out our Twitter feed from ISBM Basel at http://www.jalview.org/ and see if you spot the magician from Minnesota!

Email signature

University of Dundee shield logo

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

University of Dundee FacebookUniversity of Dundee TwitterUniversity of Dundee LinkedInUniversity of Dundee YouTubeUniversity of Dundee InstagramUniversity of Dundee Snapchat

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 Atkinson, Samantha saatkinson@mcw.edu
Sent: 24 July 2019 16:13:01
To: jalview-discuss@jalview.org jalview-discuss@jalview.org
Subject: [Jalview-discuss] Problem with sequence features file

Hello,

I have an assembly done with Clustal Omega web portal (.clustal_num file) that I imported into Jalview v. 2.11.0. Using the instructions here (http://www.jalview.org/help/html/features/featuresFormat.html) I am trying to import features into the alignment and have run into problems. Nothing is imported regardless of how I try and load the features (either drag and drop on alignment or File → Load Features/Annotations) or if I have the GFF3 section in my file. I also tried converting my clustal_num file to a .aln file and that did not solve the issue.

I have attached my Sequences Features File here in case that’s useful. Any assistance in getting the features imported would be greatly appreciated!

Thanks,

Samantha

Samantha Atkinson, PhD

Bioinformatics Analyst III

Center for Microbiome Research

Microbiology & Immunology

Medical College of Wisconsin

8701 Watertown Plank

Milwaukee, WI 53226

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

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