how to see species names

roisin_mcallister · 5 July 2019 15:16

Hi
I have a MSA (that has the species names included in the seq names)
I can’t get JalView to allow me to see them. I can manually go in and edit the name, but is there a better way?
Roisin

g_m_carstairs · 5 July 2019 15:21

Hello Roisin,

Could you explain a bit more “I can’t get JalView to allow me to see them.”?

Is there an error happening, or is it just that the names are too long to see?

If the latter, you can drag the name panel to be wider - put the cursor just above the top sequence name until it changes to a ‘drag cursor’.

You can also change the font size from the Font menu (if that helps).

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 roisin mcallister doirerosie@gmail.com
Sent: 05 July 2019 16:16:33
To: jalview-discuss@jalview.org
Subject: [Jalview-discuss] how to see species names

Hi
I have a MSA (that has the species names included in the seq names)
I can’t get JalView to allow me to see them. I can manually go in and edit the name, but is there a better way?
Roisin

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

g_m_carstairs · 6 July 2019 08:55

Hi Roisin,

When Jalview reads FASTA (and other format) sequence data, it splits the sequence identifier into an id (everything before the first space) and description (everything after the first space).

As this doesn’t seem to be part of the FASTA specification, we could maybe consider offering an option to treat the whole string as the id, but until then there is no easy way in the application to ‘recombine’ them in the id.

What you could do as a workaround is to run this Groovy script (Tools | Open Groovy Console):

al = jalview.bin.Jalview.currentAlignFrame.viewport.alignment
for (seq in al.sequences)
{
seq.name = seq.name + " " + seq.description
}

And then click in the alignment to refresh the display.

This should simply concatenate the description to the sequence name.

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: roisin mcallister doirerosie@gmail.com
Sent: 05 July 2019 16:38:28
To: Mungo Carstairs (Staff)
Subject: Re: [Jalview-discuss] how to see species names

Hi Mungo
thanks for speedy reply! No error and I have pulled the panel out wider. I attach so you can see what I mean. The species name is “there” if I point to it with cursor…but I would like it displayed in name as well if poss.
Roisin

On Fri, Jul 5, 2019 at 4:21 PM Mungo Carstairs (Staff) <g.m.carstairs@dundee.ac.uk> wrote:

Hello Roisin,

Could you explain a bit more “I can’t get JalView to allow me to see them.”?

Is there an error happening, or is it just that the names are too long to see?

If the latter, you can drag the name panel to be wider - put the cursor just above the top sequence name until it changes to a ‘drag cursor’.

You can also change the font size from the Font menu (if that helps).

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 roisin mcallister <doirerosie@gmail.com>
Sent: 05 July 2019 16:16:33
To: jalview-discuss@jalview.org
Subject: [Jalview-discuss] how to see species names

Hi
I have a MSA (that has the species names included in the seq names)
I can’t get JalView to allow me to see them. I can manually go in and edit the name, but is there a better way?
Roisin

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

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

j_procter · 7 July 2019 08:30

Hello Roisin

Just to follow up here… once you have run the script I’d recommend right-aligning the sequence IDs via the format menu so the species suffix is always visible.

Supporting species labels is a long standing goal that we will shortly start work on as part of our next major release, 2.12, so hopefully you’ll only need to use this script for a few months!

Jim.

···

On Sat, 6 Jul 2019, 09:55 Mungo Carstairs (Staff), <g.m.carstairs@dundee.ac.uk> wrote:

Hi Roisin,

When Jalview reads FASTA (and other format) sequence data, it splits the sequence identifier into an id (everything before the first space) and description (everything after the first space).

As this doesn’t seem to be part of the FASTA specification, we could maybe consider offering an option to treat the whole string as the id, but until then there is no easy way in the application to ‘recombine’ them in the id.

What you could do as a workaround is to run this Groovy script (Tools | Open Groovy Console):

al = jalview.bin.Jalview.currentAlignFrame.viewport.alignment
for (seq in al.sequences)
{
seq.name = seq.name + " " + seq.description
}

And then click in the alignment to refresh the display.

This should simply concatenate the description to the sequence name.

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: roisin mcallister <doirerosie@gmail.com>
Sent: 05 July 2019 16:38:28
To: Mungo Carstairs (Staff)
Subject: Re: [Jalview-discuss] how to see species names

Hi Mungo
thanks for speedy reply! No error and I have pulled the panel out wider. I attach so you can see what I mean. The species name is “there” if I point to it with cursor…but I would like it displayed in name as well if poss.
Roisin

On Fri, Jul 5, 2019 at 4:21 PM Mungo Carstairs (Staff) <g.m.carstairs@dundee.ac.uk> wrote:

Hello Roisin,

Could you explain a bit more “I can’t get JalView to allow me to see them.”?

Is there an error happening, or is it just that the names are too long to see?

If the latter, you can drag the name panel to be wider - put the cursor just above the top sequence name until it changes to a ‘drag cursor’.

You can also change the font size from the Font menu (if that helps).

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 roisin mcallister <doirerosie@gmail.com>
Sent: 05 July 2019 16:16:33
To: jalview-discuss@jalview.org
Subject: [Jalview-discuss] how to see species names

Hi
I have a MSA (that has the species names included in the seq names)
I can’t get JalView to allow me to see them. I can manually go in and edit the name, but is there a better way?
Roisin

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

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

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