Error with CCMgen --tree-newick about ccmgen HOT 3 CLOSED

Thank you for your answer!

I wrote this little code :

import uuid
from Bio import Phylo
import sys

def modify_clades(clade_root,pos_msa):
    b = clade_root.clades
    if len(b)>0:
        for clade in b:
            clade.name = str(uuid.uuid1())
            modify_clades(clade,pos_msa)
    else:
        clade_root.name = str(pos_msa[0])
        pos_msa[0] += 1

def write_new_tree_for_ccmgen(file_tree, file_new_tree):
    print("Tree used : ", file_tree)
    tree = Phylo.read(file_tree,"newick")
    pos_msa = [0]
    modify_clades(tree.clade, pos_msa)
    tree.clade.name = "root"
    tree.clade.branch_length = 0
    print("New Tree to use : ", file_new_tree)
    tree = Phylo.write(tree,file_new_tree,"newick")

You just have to do : write_new_tree_for_ccmgen(file_tree,file_new_tree)
If anyone want to use it, feel free to do it !

from ccmgen.

Link for the file if you want to reproduce the error

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Hi @odannis,

CCMgen is a bit restrictive when it comes to the newick format. As you already realised, the root node's label is root, the leaf nodes need to be integers that represent the position in the MSA and the internal nodes have to be named, but the name itself is not of importance. The following would be a valid input to CCMgen. Here the internal nodes were assigned random uuids.

(((0:0.39069,1:0.31737)dbf15fd9-b633-4ef2-ba1b-7a53968eb62d:0.27912,(2:0.40812,3:0.50920)fb32eeb4-513a-4063-ab10-ddbad71e5d78:0.39598)c193ccc3-e1a6-431a-acce-068fa70738a2:0.36127,((4:0.30630,5:0.30630)b9c4a9dd-57e1-4e84-b134-e748b5be9b3a:0.27982,(6:0.51569,7:0.42195)9f60b3ad-ac66-420d-bfe8-394bd2f446ed:0.27956)7c63c71a-cb6c-4c37-869a-326162c9282c:0.11241)root:0.00000;

I feel like the easiest solution is to write a short script that reads in the newick file from fasttree2, reformats it according to these constraints and writes it out again. This should not take more than 10-20 lines of code, I feel.

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