Custom truncation of GtDB tree

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Andrzej Zielezinski

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Sep 12, 2021, 1:09:36 PMSep 12
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Dear DendroPy Users,

I'm trying to truncate the GtDB tree of Bacteria to retain only selected phyla and remove other phyla (with all their descendants) from the tree. In addition, I would like to further truncate the tree to keep all taxa of the selected phyla down to the order level (remove everything below order).

I spent hours trying to get this work, but failed. Here is what I have so far:

import dendropy
from biolib.newick import parse_label

PHYLA_TO_RETAIN = set(['p__Patescibacteria', 'p__Planctomycetota'])

tree = dendropy.Tree.get_from_path('bac120.tree', 
                                    schema='newick', 
                                    rooting='force-rooted', 
                                    preserve_underscores=True)

taxa_in_tree = set()
for node in tree.postorder_node_iter():
    if not node.is_leaf():
        support, taxon, _auxiliary_info = parse_label(node.label)
        if taxon in PHYLA_TO_RETAIN:
            for leaf in node.leaf_iter():
                taxa_in_tree.add(leaf.taxon)
            PHYLA_TO_RETAIN.remove(taxon)
                
    if not PHYLA_TO_RETAIN:
        break

tree.retain_taxa(taxa_in_tree)

tree.write_to_path('tree.newick', 
                schema='newick', 
                suppress_rooting=True, 
                unquoted_underscores=True)

I can also provide the list of orders to retain/remove.

Please help :)
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