Hi there.
I’d like to retrieve the percent identity and conservation scores for an alignment as plain text files.
Since Jalview calculates these values to display in the annotations at the bottom of the alignment window, I was hoping there would be a simple way to output the scores, but I’ve yet to find one. Can this be done?
If not, I’d love to see this feature added to Jalview, and, in the interim, is there another program that can output identity (and conservation) scores as plain text?
Thanks for your help!
-Joel
Hi Joel.
I'd like to retrieve the percent identity and conservation scores for an alignment as plain text files.
Ok.
Since Jalview calculates these values to display in the annotations at the bottom of the alignment window, I was hoping there would be a simple way to output the scores, but I've yet to find one. Can this be done?
There are two ways to output this information, The Export annotations entry in the File menu of the Alignment window will let you save a jalview annotations file that contains all the annotation data for the alignment. Alternately, you can save a specific annotation row as a CSV file from the annotation row menu - just right click on the annotation row's label and select 'export annotation' which will eventually open a text box containing the data.
Is that what you meant ?
Jim.
···
On 30/01/2011 05:40, Joel Guenther wrote:
--
-------------------------------------------------------------------
J. B. Procter (JALVIEW/ENFIN) Barton Bioinformatics Research Group
Phone/Fax:+44(0)1382 388734/345764 http://www.compbio.dundee.ac.uk
The University of Dundee is a Scottish Registered Charity, No. SC015096.
Hi, Jim, and thanks for your reply.
It seems like exporting the annotations should give me what I need, but I’m having a bit of trouble.
When I right-click on the word “Consensus,” the item at the bottom of the popup menus is “Copy Consensus Sequence,” but this appears to be broken. I’ve tried both right- and left-clicking on “Copy Consensus Sequence,” but nothing gets copied. Am I missing something? I’m using Jalview 2.6.1 (Version 11 according to the “About Jalview” menu) on Mac OS X 10.6.6.
Ideally, I’d like to get a list of the consensus residue for each column and it’s percent identity. Although I can imagine that knowing what the other residues with lower conservation might be within a column, I want to start simple, and I don’t how to get rid of that additional information that I don’t want.
I seem to be trapped in text file editing purgatory 
-Joel
···
On Sun, Jan 30, 2011 at 5:37 AM, Jim Procter <jprocter@compbio.dundee.ac.uk> wrote:
Hi Joel.
On 30/01/2011 05:40, Joel Guenther wrote:
I’d like to retrieve the percent identity and conservation scores for
an alignment as plain text files.
Ok.
Since Jalview calculates these values to display in the annotations at
the bottom of the alignment window, I was hoping there would be a
simple way to output the scores, but I’ve yet to find one. Can this be
done?
There are two ways to output this information, The Export annotations
entry in the File menu of the Alignment window will let you save a
jalview annotations file that contains all the annotation data for the
alignment. Alternately, you can save a specific annotation row as a CSV
file from the annotation row menu - just right click on the annotation
row’s label and select ‘export annotation’ which will eventually open a
text box containing the data.
Is that what you meant ?
Jim.
–
J. B. Procter (JALVIEW/ENFIN) Barton Bioinformatics Research Group
Phone/Fax:+44(0)1382 388734/345764 http://www.compbio.dundee.ac.uk
The University of Dundee is a Scottish Registered Charity, No. SC015096.
Jalview-discuss mailing list
Jalview-discuss@jalview.org
http://lists.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss
D’oh!
I seem to have solved my own problem. The key was switching to the Jalview format for annotation exporting.
All I needed to do was:
- Right-click on Consensus
- Export using the Jalview format
- Delete everything from the text output through the word “PID”
- Replace All pipes (|) with line breaks (\r)
- Replace All spaces ( ) with commas (,)
- Save as a csv file
- Import into Excel
Done!
-Joel
···
On Sun, Jan 30, 2011 at 9:17 PM, Joel Guenther <guenthej@gmail.com> wrote:
Hi, Jim, and thanks for your reply.
It seems like exporting the annotations should give me what I need, but I’m having a bit of trouble.
When I right-click on the word “Consensus,” the item at the bottom of the popup menus is “Copy Consensus Sequence,” but this appears to be broken. I’ve tried both right- and left-clicking on “Copy Consensus Sequence,” but nothing gets copied. Am I missing something? I’m using Jalview 2.6.1 (Version 11 according to the “About Jalview” menu) on Mac OS X 10.6.6.
Ideally, I’d like to get a list of the consensus residue for each column and it’s percent identity. Although I can imagine that knowing what the other residues with lower conservation might be within a column, I want to start simple, and I don’t how to get rid of that additional information that I don’t want.
I seem to be trapped in text file editing purgatory
-Joel
On Sun, Jan 30, 2011 at 5:37 AM, Jim Procter <jprocter@compbio.dundee.ac.uk> wrote:
Hi Joel.
On 30/01/2011 05:40, Joel Guenther wrote:
I’d like to retrieve the percent identity and conservation scores for
an alignment as plain text files.
Ok.
Since Jalview calculates these values to display in the annotations at
the bottom of the alignment window, I was hoping there would be a
simple way to output the scores, but I’ve yet to find one. Can this be
done?
There are two ways to output this information, The Export annotations
entry in the File menu of the Alignment window will let you save a
jalview annotations file that contains all the annotation data for the
alignment. Alternately, you can save a specific annotation row as a CSV
file from the annotation row menu - just right click on the annotation
row’s label and select ‘export annotation’ which will eventually open a
text box containing the data.
Is that what you meant ?
Jim.
–
J. B. Procter (JALVIEW/ENFIN) Barton Bioinformatics Research Group
Phone/Fax:+44(0)1382 388734/345764 http://www.compbio.dundee.ac.uk
The University of Dundee is a Scottish Registered Charity, No. SC015096.
Jalview-discuss mailing list
Jalview-discuss@jalview.org
http://lists.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss
Sorry for the email blitz…
Slight correction to my procedure:
- Right-click on Consensus
- Export using the Jalview format
- Delete everything from the text output through the word “PID”
- Replace All pipes (|) with line breaks (\r)
- Replace All spaces ( ) with commas (,)
- Replace All semi-colons (
with nothing
- Save as a csv file
- Import into Excel
-Joel
···
On Sun, Jan 30, 2011 at 9:31 PM, Joel Guenther <guenthej@gmail.com> wrote:
D’oh!
I seem to have solved my own problem. The key was switching to the Jalview format for annotation exporting.
All I needed to do was:
- Right-click on Consensus
- Export using the Jalview format
- Delete everything from the text output through the word “PID”
- Replace All pipes (|) with line breaks (\r)
- Replace All spaces ( ) with commas (,)
- Save as a csv file
- Import into Excel
Done!
-Joel
On Sun, Jan 30, 2011 at 9:17 PM, Joel Guenther <guenthej@gmail.com> wrote:
Hi, Jim, and thanks for your reply.
It seems like exporting the annotations should give me what I need, but I’m having a bit of trouble.
When I right-click on the word “Consensus,” the item at the bottom of the popup menus is “Copy Consensus Sequence,” but this appears to be broken. I’ve tried both right- and left-clicking on “Copy Consensus Sequence,” but nothing gets copied. Am I missing something? I’m using Jalview 2.6.1 (Version 11 according to the “About Jalview” menu) on Mac OS X 10.6.6.
Ideally, I’d like to get a list of the consensus residue for each column and it’s percent identity. Although I can imagine that knowing what the other residues with lower conservation might be within a column, I want to start simple, and I don’t how to get rid of that additional information that I don’t want.
I seem to be trapped in text file editing purgatory
-Joel
On Sun, Jan 30, 2011 at 5:37 AM, Jim Procter <jprocter@compbio.dundee.ac.uk> wrote:
Hi Joel.
On 30/01/2011 05:40, Joel Guenther wrote:
I’d like to retrieve the percent identity and conservation scores for
an alignment as plain text files.
Ok.
Since Jalview calculates these values to display in the annotations at
the bottom of the alignment window, I was hoping there would be a
simple way to output the scores, but I’ve yet to find one. Can this be
done?
There are two ways to output this information, The Export annotations
entry in the File menu of the Alignment window will let you save a
jalview annotations file that contains all the annotation data for the
alignment. Alternately, you can save a specific annotation row as a CSV
file from the annotation row menu - just right click on the annotation
row’s label and select ‘export annotation’ which will eventually open a
text box containing the data.
Is that what you meant ?
Jim.
–
J. B. Procter (JALVIEW/ENFIN) Barton Bioinformatics Research Group
Phone/Fax:+44(0)1382 388734/345764 http://www.compbio.dundee.ac.uk
The University of Dundee is a Scottish Registered Charity, No. SC015096.
Jalview-discuss mailing list
Jalview-discuss@jalview.org
http://lists.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss