[Bioperl-l] Fw: Bootstrap, root, reroot...
Mark A. Jensen
maj at fortinbras.us
Thu Jul 9 21:55:23 UTC 2009
up to the list, too--
----- Original Message -----
From: "Mark A. Jensen" <maj at fortinbras.us>
To: "Tristan Lefebure" <tristan.lefebure at gmail.com>
Sent: Thursday, July 09, 2009 3:37 PM
Subject: Re: [Bioperl-l] Bootstrap, root, reroot...
> I'll bet you're right-- I'll put this in as a comment-- thanks!
> ----- Original Message -----
> From: "Tristan Lefebure" <tristan.lefebure at gmail.com>
> To: "BioPerl List" <bioperl-l at lists.open-bio.org>
> Sent: Thursday, July 09, 2009 3:18 PM
> Subject: Re: [Bioperl-l] Bootstrap, root, reroot...
>
>
>>I just add a quick look at the reroot() function of TreeFunctionsI, and it
>> looks like that what should be done for the bootstrap scores is what is
>> already done for the branch lengths. See this loop starting line 954:
>>
>> # reverse the ancestor & children pointers
>> my $former_anc = $tmp_node->ancestor;
>> my @path_from_oldroot = ($self->get_lineage_nodes($tmp_node),
>> $tmp_node);
>> for (my $i = 0; $i < @path_from_oldroot - 1; $i++) {
>> my $current = $path_from_oldroot[$i];
>> my $next = $path_from_oldroot[$i + 1];
>> $current->remove_Descendent($next);
>> $current->branch_length($next->branch_length);
>> $next->add_Descendent($current);
>> }
>>
>> It makes sense to me to treat bootstrap and branch lenght in a similar way:
>> the branch lengths are stored inside the node object, but as the bootstrap,
>> they really are branch attributes... Nope?
>>
>> -Tristan
>>
>> On Thu, Jul 9, 2009 at 2:30 PM, Tristan Lefebure <tristan.lefebure at gmail.com
>>> wrote:
>>
>>> Done. bug #2877.
>>> -Tristan
>>>
>>> On Thursday 09 July 2009 14:02:01 Mark A. Jensen wrote:
>>> > Hi Tristan--
>>> > Would you enter this in bugzilla? I did an overhaul of
>>> > the root/reroot a while back, and maybe you're running
>>> > into some stuff I need to check out. Thanks a lot-
>>> > Mark
>>> > ----- Original Message -----
>>> > From: "Tristan Lefebure" <tristan.lefebure at gmail.com>
>>> > To: "BioPerl List" <bioperl-l at lists.open-bio.org>
>>> > Sent: Thursday, July 09, 2009 11:50 AM
>>> > Subject: [Bioperl-l] Bootstrap, root, reroot...
>>> >
>>> > > Hello,
>>> > >
>>> > > I have been bumping into problems while rerooting trees
>>> > > that contained bootstrap scores. Basically, after
>>> > > re-rooting the tree, some scores end-up at the wrong
>>> > > place (i.e. node) and some nodes lose their score. I
>>> > > found this thread from Bank Beszter, back in 2007, that
>>> > > exactly explains the same problems:
>>> > >
>>> > > http://lists.open-bio.org/pipermail/bioperl-l/2007-
>>> > > May/025599.html
>>> > >
>>> > > I attach a script that reproduces the bug and
>>> > > implements the fix that Bank described (at least this
>>> > > is my understanding, and it works on this example):
>>> > >
>>> > >
>>> > > #! /usr/bin/perl
>>> > >
>>> > > use strict;
>>> > > use warnings;
>>> > > use Bio::TreeIO;
>>> > >
>>> > >
>>> > > my $in = Bio::TreeIO->new(-format => 'newick',
>>> > > -fh => \*DATA,
>>> > > -internal_node_id => 'bootstrap');
>>> > >
>>> > > my $out = Bio::TreeIO->new(-format => 'newick', -file
>>> > > => ">out.tree");
>>> > >
>>> > > while( my $t = $in->next_tree ){
>>> > > my $old_root = $t->get_root_node();
>>> > > my ($b) = $t->find_node(-id =>"B");
>>> > > my $b_anc = $b->ancestor;
>>> > > $out->write_tree($t);
>>> > >
>>> > > #reroot with B -> wrong, and the tree is kind of weird
>>> > > $t->reroot($b);
>>> > > $out->write_tree($t);
>>> > >
>>> > > #reroot with B ancestor -> wrong
>>> > > $t->reroot($b_anc);
>>> > > $out->write_tree($t);
>>> > >
>>> > > #a fix, following Bank Beszteri description
>>> > > my $node = $old_root;
>>> > > while (my $anc_node = $node->ancestor) {
>>> > > $node->bootstrap($anc_node->bootstrap());
>>> > > $anc_node->bootstrap('');
>>> > > $node = $anc_node;
>>> > > }
>>> > > $out->write_tree($t); #->good this time
>>> > > }
>>> > >
>>> > >
>>> > > __DATA__
>>> > > (A:52,(B:46,C:50)68:11,D:70);
>>> > >
>>> > >
>>> > > Here is the output:
>>> > >
>>> > > (A:52,(B:46,C:50)68:11,D:70);
>>> > > ((C:50,(A:52,D:70):11)68:46)B;
>>> > > (B:46,C:50,(A:52,D:70):11)68;
>>> > > (B:46,C:50,(A:52,D:70)68:11);
>>> > >
>>> > >
>>> > > Tree #2 and #3 have the score 68 moved to the wrong
>>> > > node, while tree #4 is OK. (BTW tree #2 is really
>>> > > weird, except if B, is the real ancestor (a fossil ?),
>>> > > it really does not make much sense to me).
>>> > >
>>> > > My understanding here is that the problem is linked to
>>> > > the well-known difficulty to differentiate node from
>>> > > branch labels in newick trees. Bootstrap scores are
>>> > > branch attributes not node attributes, but since
>>> > > Bio::TreeI has no branch/edge/bipartition object they
>>> > > are attached to a node, and in fact reflects the
>>> > > bootstrap score of the ancestral branch leading to that
>>> > > node. Troubles naturally come when you are dealing with
>>> > > an unrooted tree or reroot a tree: a child can become
>>> > > an ancestor, and, if the bootstrap scores is not moved
>>> > > from the old child to the new child, it will end up
>>> > > attached at the wrong place (i.e. wrong node).
>>> > >
>>> > > I see several fix to that:
>>> > >
>>> > > 1- incorporate Bank's fix into the root() method. I.e.
>>> > > if there is bootstrap score, after re-rooting, the one
>>> > > on the old to new ancestor path, should be moved to the
>>> > > right node.
>>> > >
>>> > > 2- Modify the way trees are stored in bioperl to
>>> > > incorporate branch/edge/bipartition object, and move
>>> > > the bootstrap scores to them. That won't be easy and
>>> > > will break many things...
>>> > >
>>> > >
>>> > > What do you think?
>>> > >
>>> > > --Tristan
>>> > >
>>> > >
>>> > >
>>> > >
>>> > >
>>> > >
>>> > >
>>> > > _______________________________________________
>>> > > Bioperl-l mailing list
>>> > > Bioperl-l at lists.open-bio.org
>>> > > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>>
>>>
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