Jason Stajich | 17 Jul 22:13 2013

Re: Checking a tree input

It depends on what format the bootstraps are stored in - are they as internal node labels or encoded in the ID
string or encoded in the length of the branches?

Because there isn't an explicit format - there are variants of it for newick -  you can move them
automatically passing in '-bootstrap_style' => 'traditional')  when initializating the parser.
or you can move them explicitly 

copy them from ID to boostrap slot in the objects after you have created it.
for my $node ( grep { ! $_->is_Leaf } $tree->get_nodes ) {

Or you can use the connivence function which does the same thing.

Presumably these internal node IDs will be empty when there is no bootstrap so you can check them after the
fact for your other use case when there are no boostraps.

On Jul 14, 2013, at 1:45 AM, soungalo <soungalo <at> walla.com> wrote:

> Hi there,
> Does anyone know if I can do the following:
> given an input file, check whether it is a newick tree or not, and if it is,
> check if it has bootstrap values.
> Regarding the bootstraps, I tried reading previous posts here, but I didn't
> get it - using the TreeIO module, the $node->bootstrap method keeps giving
> undefined values. In some trees, the bootstrap values are in the id field.
> Can you explain how to work with bootstraps ?
> Thanks!
> --
> View this message in context: http://bioperl.996286.n3.nabble.com/Checking-a-tree-input-tp17041.html
> Sent from the Bioperl-L mailing list archive at Nabble.com.
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l <at> lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Jason Stajich
jason.stajich <at> gmail.com
jason <at> bioperl.org