Skbio with Tree

[Zach]

Hi all,

I am new to this forum as well as python, and would be grateful for any help. I am working with a tree for my analyses and it does not seem to be in Newick format. I am not sure if this could be the reason for the error. I have run the 1st 2 commands below without any problems:

tree_dir = abspath('/home/allio/Documents/Zach_Master/Q2-all-gut-skin-oral/trees/')
host_tree_fp = 'MamPhy_fullPosterior_BDvr_Completed_5911sp_topoCons_NDexp_MCC_v2_target.tre'

However, when I run the command below:

host_tree = sk.TreeNode.read(join(tree_dir, host_tree_fp), convert_underscores=False)

I receive the error message:

Error:
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/allio/bin/anaconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/skbio/io/registry.py", line 652, in read
    return registry.read(file, into=cls, format=format, **kwargs)
  File "/home/allio/bin/anaconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/skbio/io/registry.py", line 513, in read
    return self._read_ret(file, format, into, verify, kwargs)
  File "/home/allio/bin/anaconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/skbio/io/registry.py", line 519, in _read_ret
    io_kwargs)
  File "/home/allio/bin/anaconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/skbio/io/registry.py", line 539, in _init_reader
    fmt, skwargs = self.sniff(file, **io_kwargs)
  File "/home/allio/bin/anaconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/skbio/io/registry.py", line 431, in sniff
    % file)
skbio.io._exception.UnrecognizedFormatError: Could not detect the format of <_io.BufferedReader name='/home/allio/Documents/Zach_Master/Q2-all-gut-skin-oral/trees/MamPhy_fullPosterior_BDvr_Completed_5911sp_topoCons_NDexp_MCC_v2_target.tre'>

Why is this occurring, and what are the possible solutions to this? Cheers!

[buran]

it looks MamPhy_fullPosterior_BDvr_Completed_5911sp_topoCons_NDexp_MCC_v2_target.tre is not in format recognozed by scikit-bio
And it's good to mention what packages you use / show full code, incl. the imports, etc. (minimal reproducible example)

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supported file formats:
http://scikit-bio.org/docs/latest/io.htm...e-skbio.io