KeyError raised when extracting barcodes from custom PB tree.

[watronfire]

Hey y'all,

I'm attempting to extract lineage barcodes from a custom cholera PB tree using the following freyja command:

freyja barcode-build --pb o1_cholera.no_missing.pb --outdir freyja-barcodes/ --noncl

Here is the tree: o1_cholera.no_missing.pb.zip

However, this raises a KeyError during the separating combined splits step. See the following traceback:

Getting outbreak data
Downloading a new global tree
Converting tree info to barcodes
Reading custom tree at: o1_cholera.no_missing.pb
Building barcodes from global phylogenetic tree
separating combined splits
Traceback (most recent call last):
  File "/PHShome/nm104/mambaforge/envs/phonebook/bin/freyja", line 10, in <module>
    sys.exit(cli())
  File "/PHShome/nm104/mambaforge/envs/phonebook/lib/python3.9/site-packages/click/core.py", line 1157, in __call__
    return self.main(*args, **kwargs)
  File "/PHShome/nm104/mambaforge/envs/phonebook/lib/python3.9/site-packages/click/core.py", line 1078, in main
    rv = self.invoke(ctx)
  File "/PHShome/nm104/mambaforge/envs/phonebook/lib/python3.9/site-packages/click/core.py", line 1688, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/PHShome/nm104/mambaforge/envs/phonebook/lib/python3.9/site-packages/click/core.py", line 1434, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/PHShome/nm104/mambaforge/envs/phonebook/lib/python3.9/site-packages/click/core.py", line 783, in invoke
    return __callback(*args, **kwargs)
  File "/PHShome/nm104/mambaforge/envs/phonebook/lib/python3.9/site-packages/freyja/_cli.py", line 312, in barcode_build
    df_barcodes = convert_to_barcodes(df)
  File "/PHShome/nm104/mambaforge/envs/phonebook/lib/python3.9/site-packages/freyja/convert_paths2barcodes.py", line 32, in convert_to_barcodes
    df_barcodes = df_barcodes.drop(columns='')
  File "/PHShome/nm104/mambaforge/envs/phonebook/lib/python3.9/site-packages/pandas/core/frame.py", line 5581, in drop
    return super().drop(
  File "/PHShome/nm104/mambaforge/envs/phonebook/lib/python3.9/site-packages/pandas/core/generic.py", line 4788, in drop
    obj = obj._drop_axis(labels, axis, level=level, errors=errors)
  File "/PHShome/nm104/mambaforge/envs/phonebook/lib/python3.9/site-packages/pandas/core/generic.py", line 4830, in _drop_axis
    new_axis = axis.drop(labels, errors=errors)
  File "/PHShome/nm104/mambaforge/envs/phonebook/lib/python3.9/site-packages/pandas/core/indexes/base.py", line 7070, in drop
    raise KeyError(f"{labels[mask].tolist()} not found in axis")
KeyError: "[''] not found in axis"

The specific line the error is referencing is below, and I believe the issue is that Freyja assumes the barcode dataframe will contain a column with the name "".

Freyja/freyja/convert_paths2barcodes.py

Line 32 in af5f46a

df_barcodes = df_barcodes.drop(columns='')

However, if I put a breakpoint before this statement and debug, I find that the dataframe generated by my tree doesn't have this empty column. Additionally, if I wrap the line in a conditional (if "" in df.columns:), the error is not raised and the command runs without a issue, and I assume the barcodes are chill.

I'll make a PR with the fix now, but wanted to post this issue so its tracked, if y'all want to explore my PB (attached) or whatever.

[watronfire]

My environment, if it matters:

• python 3.9.19
• pandas 2.2.3
• usher 0.6.3
• freyja 1.5.2