HMM database about metator HOT 3 CLOSED

Hi,

I have reupload the hmm database which was missing. It's available at this link: https://github.com/koszullab/metaTOR/raw/master/metator/data/hmm_databases.tgz.

Best,

from metator.

Hi,

Thanks for the reply. This problem has been solved. However, I get into trouble again in the final binning step.

**** Starting binning ****
Drawing enrichment vs. size plots...
Drawing distribution violinplot...
Extracting bin subnetworks and matrices...
INFO :: Loading partition...
INFO :: Loading network...
Extracting bin FASTA files...
WARNING :: /home/Anaconda3/lib/python3.7/site-packages/metator/bin/../scripts/bins.py:216: VisibleDeprecationWarning: Reading unicode strings without specifying the
encoding argument is deprecated. Set the encoding, use None for the system default.
zip(*np.genfromtxt(partition_file, usecols=(0, 1), dtype=None))

Traceback (most recent call last):
File "/home/Anaconda3/lib/python3.7/site-packages/metator/bin/../scripts/bins.py", line 447, in
main()
File "/home/Anaconda3/lib/python3.7/site-packages/metator/bin/../scripts/bins.py", line 438, in main
chunk_size=chunk_size,
File "/home/Anaconda3/lib/python3.7/site-packages/metator/bin/../scripts/bins.py", line 231, in extract_fasta
fields = name.split("_")
TypeError: a bytes-like object is required, not 'str'

Appreciate some suggestions.

Best

from metator.

Hi,

Thanks for the report. Indeed, the argument of one function were deprecated, we have corrected the code, so hopefully it should work if you upgrade metator.

Best,

from metator.