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View Code? Open in Web Editor NEWPython package to obtain, parse and explore biological taxonomies (GTDB, NCBI, Silva, Greengenes, OTT)
Home Page: https://pirovc.github.io/multitax/
License: MIT License
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Skip empty lines
Skip empty lines when parsing tax. files, as reported here (pirovc/ganon#282)
urllib error
Hello, I have used the multitax package before to mainly translate taxon ids to the taxon name (e.g. 3702 -> Arabidopsis thaliana). When I run code that previously was working, now I get the following error:
>>> from multitax import NcbiTx
>>> ncbi_tx = NcbiTx()
Traceback (most recent call last):
File "/zfs/omics/personal/asanche2/miniconda3/envs/aa/lib/python3.10/urllib/request.py", line 1555, in ftp_open
host = socket.gethostbyname(host)
socket.gaierror: [Errno -2] Name or service not known
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/zfs/omics/personal/asanche2/miniconda3/envs/aa/lib/python3.10/site-packages/multitax/ncbitx.py", line 15, in __init__
super().__init__(**kwargs)
File "/zfs/omics/personal/asanche2/miniconda3/envs/aa/lib/python3.10/site-packages/multitax/multitax.py", line 82, in __init__
fhs = download_files(urls=urls if urls else self._default_urls,
File "/zfs/omics/personal/asanche2/miniconda3/envs/aa/lib/python3.10/site-packages/multitax/utils.py", line 71, in download_files
fileobj=load_url_mem(url), mode='r:gz')
File "/zfs/omics/personal/asanche2/miniconda3/envs/aa/lib/python3.10/site-packages/multitax/utils.py", line 107, in load_url_mem
urlstream = urllib.request.urlopen(url)
File "/zfs/omics/personal/asanche2/miniconda3/envs/aa/lib/python3.10/urllib/request.py", line 216, in urlopen
return opener.open(url, data, timeout)
File "/zfs/omics/personal/asanche2/miniconda3/envs/aa/lib/python3.10/urllib/request.py", line 519, in open
response = self._open(req, data)
File "/zfs/omics/personal/asanche2/miniconda3/envs/aa/lib/python3.10/urllib/request.py", line 536, in _open
result = self._call_chain(self.handle_open, protocol, protocol +
File "/zfs/omics/personal/asanche2/miniconda3/envs/aa/lib/python3.10/urllib/request.py", line 496, in _call_chain
result = func(*args)
File "/zfs/omics/personal/asanche2/miniconda3/envs/aa/lib/python3.10/urllib/request.py", line 1557, in ftp_open
raise URLError(msg)
urllib.error.URLError: <urlopen error [Errno -2] Name or service not known>
Library returns 404
Hi, I just ran these three commands, and it raises an Exception:
xapple@local ~ $ python3 -m pip install --user multitax
xapple@local ~ $ ipython3
In [1]: from multitax import GtdbTx
In [2]: tax = GtdbTx()
HTTPError: HTTP Error 404: Not Found
Translation between Silva and NCBI
Hi there,
The translation table says that from Silva to NCBI is fully implemented and from NCBI to Silva is partially implemented. And yet I get the following errors.
from multitax import SilvaTx, NcbiTx
silva_tax = SilvaTx()
ncbi_tax = NcbiTx()
ncbi_tax.build_translation(silva_tax)
# /path/to/multitax/ncbitx.py:86: UserWarning: Translation between taxonomies [NcbiTx,SilvaTx] not yet implemented.
silva_tax.build_translation(ncbi_tax)
# /path/to/multitax/silvatx.py:17: UserWarning: Translation between taxonomies [SilvaTx,NcbiTx] not yet implemented.
Is this because the linkage data isn't available in the default data? I'm new to microbiome taxonomy, and some clarity on what linkage data is would be greatly appreciated.
Changed GTDB metadata naming and format
I was attempting to map from NCBI to GTDB taxonomy, when building translation multitax was unable to download GTDB metadata
from multitax import GtdbTx, NcbiTx
ncbi = NcbiTx()
gtdb = GtdbTx()
ncbi.build_translation(gtdb)
Exception: One or more files could not be downloaded: https://data.gtdb.ecogenomic.org/releases/latest/ar53_metadata.tar.gz, https://data.gtdb.ecogenomic.org/releases/latest/bac120_metadata.tar.gz
For r214.1, the metadata is no longer a tarball, appears to be a gzipped tsv: bac120_metadata.tsv.gz, ar53_metadta.tsv.gz. Looks like it would need some different handling in build_translation as well as that extract tar members.
I'd be happy to put together a pull request to fix, if you're interested.
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