[Jalview-discuss] "Show values in textbox" for consensus in Jalview 2.5

[Jim Procter]

Hello Hari.

I'm sorry about this - its entirely my fault. In my rush to get 2.5 
released, I didn't verify that the old CSV output that you need was 
still possible (my intention was that disabling the sequence logo 
display would change the annotation mouseover and CSV text, too, but I 
didn't finish implementing this).

Can you wait until the next release ?  I should have time to re-instate 
the old CSV export style as a bug fix to 2.5 by the end of next week.

Jim.

On 13/05/2010 14:21, hari jayaram wrote:
> Hi I have a saved alignement generated from the clustalw service at EMBL-EBI.
> When I launch Jalview from the clustalw site - I click on the
> consensus and be presented with a "Show values in textbox" option
> which then prints to a textbox the following information ( see below).
> The second line of this information which indicates the consensus
> sequence and the percentage conservation at that point.
>
> This feature is however not available in jalview 2.5 . How can I open
> any saved alignment in jalview 2.5 and obtain the  consensus
> percentage for each position in the alignment for use in another
> downstream analysis program.
>
> Thanks
> Hari
>
>
> Show values in textbox" option output:
>
>
> 0.0, 0.0, 0.0, 0.0, 5.4054055, 0.0, 0.0, 5.4054055, 0.0, 0.0, 0.0,
> 5.4054055, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
> 0.0, 18.918919, 21.621622, 18.918919, 18.918919, 21.621622, 16.216217,
> 18.918919, 21.621622, 21.621622, 29.72973, 13.513514, 16.216217,
> 27.027027, 5.4054055, 13.513514, 8.1081085, 10.810811, 13.513514,
> 16.216217, 24.324324, 48.648647, 13.513514, 0.0, 0.0, 13.513514,
> 27.027027, 37.837837, 24.324324, 16.216217, 16.216217, 21.621622,
> 18.918919, 45.945946, 37.837837, 72.97298, 32.432434, 13.513514,
> 18.918919, 48.648647, 24.324324, 27.027027, 89.189186, 5.4054055, 0.0,
> 0.0, 0.0, 0.0, 0.0, 35.135136, 40.54054, 62.162163, 29.72973,
> 37.837837, 78.37838, 21.621622, 18.918919, 35.135136, 45.945946,
> 24.324324, 0.0, 0.0, 0.0, 24.324324, 16.216217, 32.432434, 83.78378,
> 16.216217, 24.324324, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
> 0.0, 0.0, 0.0, 21.621622, 18.918919, 29.72973, 45.945946, 18.918919,
> 24.324324, 72.97298, 21.621622, 18.918919, 45.945946, 29.72973,
> 24.324324, 13.513514, 91.89189, 51.351353, 18.918919, 16.216217, 0.0,
> 54.054054, 59.45946, 29.72973, 18.918919, 5.4054055, 29.72973,
> 40.54054, 16.216217, 16.216217, 32.432434, 21.621622, 21.621622,
> 54.054054, 16.216217, 16.216217, 0.0, 0.0, 5.4054055, 5.4054055, 0.0,
> 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
> - 0%, - 0%, - 0%, - 0%, M 5%, - 0%, - 0%, I 5%, - 0%, - 0%, - 0%, K
> 5%, - 0%, - 0%, - 0%, - 0%, - 0%, - 0%, - 0%, - 0%, - 0%, - 0%, - 0%,
> - 0%, - 0%, C 18%, L 21%, E 18%, [IV] 18%, [IL] 21%, [KR] 16%, K 18%,
> L 21%, K 21%, E 29%, [KN] 13%, D 16%, G 27%, [GS] 5%, R 13%, [RT] 8%,
> I 10%, [AS] 13%, K 16%, I 24%, F 48%, [ELP] 13%, - 0%, - 0%, E 13%, L
> 27%, P 37%, D 24%, R 16%, E 16%, E 21%, V 18%, P 45%, D 37%, Y 72%, Y
> 32%, K 13%, I 18%, I 48%, K 24%, K 27%, P 89%, G 5%, - 0%, - 0%, - 0%,
> - 0%, - 0%, M 35%, D 40%, L 62%, S 29%, T 37%, I 78%, E 21%, Q 18%, K
> 35%, L 45%, E 24%, - 0%, - 0%, - 0%, S 24%, K 16%, K 32%, Y 83%, K
> 16%, S 24%, - 0%, - 0%, - 0%, - 0%, - 0%, - 0%, - 0%, - 0%, - 0%, -
> 0%, - 0%, - 0%, L 21%, A 18%, E 29%, F 45%, E 18%, A 24%, D 72%, [IV]
> 21%, E 18%, L 45%, [IM] 29%, F 24%, K 13%, N 91%, A 51%, I 18%, R 16%,
> - 0%, Y 54%, N 59%, G 29%, K 18%, R 5%, G 29%, S 40%, E 16%, L 16%, Y
> 32%, K 21%, D 21%, A 54%, [IL] 16%, E 16%, - 0%, - 0%, K 5%, V 5%, -
> 0%, - 0%, - 0%, - 0%, - 0%, - 0%, - 0%, - 0%, - 0%, - 0%, - 0%,
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J. B. Procter  (JALVIEW/ENFIN)  Barton Bioinformatics Research Group
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