[Bioperl-l] Bio::Tree development
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.
Relevant code and data demonstrate the problem also helps; submit
them as attachments after filing a bug report:
On Jan 19, 2007, at 2:53 PM, Lucia Peixoto wrote:
> 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
> 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,
> 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!
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
> Lucia Peixoto
> Department of Biology,SAS
> University of Pennsylvania
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign
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