[Bioperl-l] Bio::Tree development

Chris Fields cjfields at uiuc.edu
Fri Jan 19 15:55:21 EST 2007


You should always file any potential problems as a bug, otherwise  
we'll never know about it.

http://www.bioperl.org/wiki/Bugs

Relevant code and data demonstrate the problem also helps; submit  
them as attachments after filing a bug report:

http://bugzilla.open-bio.org/

chris

On Jan 19, 2007, at 2:53 PM, Lucia Peixoto wrote:

> Hi
>
> One of the functions missing from TreeIO that will be good to  
> implement is a
> collpase bootstrap function, meaning to collapse all nodes bellow a  
> certain
> bootstrap value
>
> I do have a bit of code to do this, however it cannot be  
> generalized until the
> bootstrap value is consistently captured by the same function, so  
> far, for the
> trees I have at least, the internal ID is the bootstrap value, but  
> that may not
> be true for all trees.Or it can be written asuming that you already  
> set the
> boostrap to the right value.
>
> The function bootstrap in Bio::Tree::NodeI never gets the bootstrap  
> right in any
> tree I've used (always newick format I am talking)
>
> just an idea,
>
> Lucia
>
>
>
> Quoting Chris Fields <cjfields at uiuc.edu>:
>
>>
>> On Jan 19, 2007, at 1:18 PM, Sendu Bala wrote:
>> ...
>>>
>>>> * General code cleanup
>>>> Making sure everything is indented according to some standard. I've
>>>> seen previously that there doesn't seem to be any real standard for
>>>> how BioPerl code should look like. I would think that it would be a
>>>> lot clearer to understand lots of the code if it was indented
>>>> properly. As it is now, the indentation depth changes between  
>>>> 2,3 and
>>>> 4 within the same file even.
>>>
>>> My own personal preference is an indent of 4 spaces.
>> ...
>>
>> Mine as well.  Some people also use tabs vs spaces (I prefer
>> spaces).  However, I think (Johan) you'll be hard-pressed to force a
>> standard there.
>>
>> You're always welcome to run it through perltidy prior to commits!
>>
>> chris
>> _______________________________________________
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>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>
>
> Lucia Peixoto
> Department of Biology,SAS
> University of Pennsylvania

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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