lineage -a

[marco-mariotti]

option -a does not work:

selenoprofiles lineage -i orthology/DI.orthology.tsv -of lineage  -a joined/DI.ali

|         selenoprofiles v4.5          Host:    Date: Wed 20 Nov 2024 06:05:49 PM CET
|-----------------------------------------------------------------------------------------------------------------------
|        Running utility: selenoprofiles lineage
1 unique names in input
input for tree: 1 taxids
building tree...DONE!


1 taxids in input
1 leaves in tree

A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
--> writing output: lineage/DI.lineage.tsv
Traceback (most recent call last):
  File "/home/mmariotti/mambaforge/envs/cnd.selenoprofiles4/bin/selenoprofiles", line 10, in <module>
    sys.exit(main())
             ^^^^^^
  File "/home/mmariotti/mambaforge/envs/cnd.selenoprofiles4/lib/python3.12/site-packages/selenoprofiles4/selenoprofiles4.py", line 1643, in main
    run_lineage(lin_opt)
  File "/home/mmariotti/mambaforge/envs/cnd.selenoprofiles4/lib/python3.12/site-packages/selenoprofiles4/selenoprofiles_lineage.py", line 426, in main
    ali = Alignment(opt["a"], fileformat="fasta")
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/mmariotti/mambaforge/envs/cnd.selenoprofiles4/lib/python3.12/site-packages/pyaln/alignment.py", line 222, in __init__
    for title, sequence in file_or_iter:
        ^^^^^^^^^^^^^^^
ValueError: too many values to unpack (expected 2)