[Bioperl-guts-l] [Bug 1822] nhx.pm does not print bootstrap values

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Mon Sep 26 16:06:32 EDT 2005


http://bugzilla.open-bio.org/show_bug.cgi?id=1822


jason at open-bio.org changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|NEW                         |RESOLVED
         Resolution|                            |FIXED




------- Comment #1 from jason at open-bio.org  2005-09-26 16:06 -------
You need to move the bootstraps over to the bootstrap slot- they are node IDs
initially for internal ids as we with newick we can distinguish between
internal node ids and bootstraps (although I do parse molphy encoded bootstraps
from the branch length where appropriate ((A:0.2,B:0.1):0.32[100])

So this code for your tree processing loop should work:

while (my $t = $in->next_tree) {
    for my $node ( grep { ! $_->is_Leaf } $t->get_nodes ) {
        $node->bootstrap($node->id) if $node->id;
    }
    $out->write_tree($t);
}




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