[Jalview-discuss] Percent identity output

[Joel Guenther]

Sorry for the email blitz...

Slight correction to my procedure:

   1. Right-click on Consensus
   2. Export using the Jalview format
   3. Delete everything from the text output through the word "PID"
   4. Replace All pipes (|) with line breaks (\r)
   5. Replace All spaces ( ) with commas (,)
   6. Replace All semi-colons (;) with nothing
   7. Save as a csv file
   8. Import into Excel

-Joel



On Sun, Jan 30, 2011 at 9:31 PM, Joel Guenther <guenthej at 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:
>
>    1. Right-click on Consensus
>    2. Export using the Jalview format
>    3. Delete everything from the text output through the word "PID"
>    4. Replace All pipes (|) with line breaks (\r)
>    5. Replace All spaces ( ) with commas (,)
>    6. Save as a csv file
>    7. Import into Excel
>
> Done!
>
> -Joel
>
>
>
>
> On Sun, Jan 30, 2011 at 9:17 PM, Joel Guenther <guenthej at 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 :-P
>>
>> -Joel
>>
>>
>>
>>
>>
>>
>>
>>
>> On Sun, Jan 30, 2011 at 5:37 AM, Jim Procter <
>> jprocter at 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 at jalview.org
>>> http://lists.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss
>>>
>>
>>
>
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