ete icon indicating copy to clipboard operation
ete copied to clipboard

`ete4 compare` command line interface is broken

Open hmontenegro opened this issue 7 months ago • 0 comments

ete4 compare fails with the simplest command from the documentation:

$ ete4 compare -t '((A,B), ((C,D),E));' '((E,(C,D)), (B,A));' '((A,B,X), (Z,((C,D),E)));'  -r '((A, B), ((C, D),E));' 
source          | ref             | E.size  | nRF     | RF      | maxRF   | src-br+ | ref-br+ | subtre+ | treekoD
==============+ | ==============+ | ======+ | ======+ | ======+ | ======+ | ======+ | ======+ | ======+ | ======+
Traceback (most recent call last):
  File "/home/program2/bin/ETE3/4.4.0/bin/ete4", line 7, in <module>
    sys.exit(main())
  File "/home/program2/bin/ETE3/4.4.0/lib64/python3.9/site-packages/ete4/tools/ete.py", line 64, in main
    _main(sys.argv)
  File "/home/program2/bin/ETE3/4.4.0/lib64/python3.9/site-packages/ete4/tools/ete.py", line 256, in _main
    args.func(args)
  File "/home/program2/bin/ETE3/4.4.0/lib64/python3.9/site-packages/ete4/tools/ete_compare.py", line 93, in run
    stree = tree_class(stree_name, format=args.src_newick_format)
  File "ete4/core/tree.pyx", line 41, in ete4.core.tree.Tree.__init__
TypeError: __init__() got an unexpected keyword argument 'format'

Python 3.9.13, ETE4 4.4.0, installed with pip.

hmontenegro avatar Sep 05 '25 13:09 hmontenegro