search

cokelaer / bioservices

Access to Biological Web Services from Python.
http://bioservices.readthedocs.io
Other
278 stars 60 forks source link

WARNING [bioservices:keggparser:119] #203

Closed raven44099 closed 2 years ago

raven44099 commented 2 years ago

I just follow the request to report the warning here. I run a line from the tutorial ( https://bioservices.readthedocs.io/en/master/kegg_tutorial.html ), which is great by the way and I like bioservices.kegg already after running 5 lines. Wow! The tutorials line is: k.get_pathway_by_gene("zap70", "hsa") The output:

WARNING [bioservices:keggparser:119]:  Found keyword SYMBOL, which has not special
    parsing for now. please report this issue with the KEGG 
    identifier (7535              CDS       T01001) into github.com/bioservices. Thanks T.C.
WARNING [bioservices:keggparser:119]:  Could not parse the entry CDS       T01001 correctly
WARNING [bioservices:keggparser:119]:  not enough values to unpack (expected 2, got 1)
Pfam  PK_Tyr_Ser-Thr Pkinase SH2 ABC1 Haspin_kinase Kdo

By the way, the github.com/bioservices is wrong, I think it should point to this issues-page.

raven44099 commented 2 years ago

I do not request you answer all my issues, but I kindly want to note an error in the line: res = s.parse_kgml_pathway("hsa04660")

Error

``` Traceback (most recent call last): File "/tmp/ipykernel_10118/2696537334.py", line 1, in res = s.parse_kgml_pathway("hsa04660") File "/home/ubuntuds64/miniconda3/lib/python3.8/site-packages/bioservices/kegg.py", line 973, in parse_kgml_pathway res = self.easyXML(self.get(pathwayId, "kgml")) File "/home/ubuntuds64/miniconda3/lib/python3.8/site-packages/bioservices/services.py", line 211, in easyXML return xmltools.easyXML(res) File "/home/ubuntuds64/miniconda3/lib/python3.8/site-packages/bioservices/xmltools.py", line 86, in __init__ self.prettify = self.soup.prettify File "/home/ubuntuds64/miniconda3/lib/python3.8/site-packages/bioservices/xmltools.py", line 98, in _get_soup self._soup = bs4.BeautifulSoup(self.data, "lxml") File "/home/ubuntuds64/miniconda3/lib/python3.8/site-packages/bs4/__init__.py", line 245, in __init__ raise FeatureNotFound( FeatureNotFound: Couldn't find a tree builder with the features you requested: lxml. Do you need to install a parser library? ```

cokelaer commented 2 years ago

@raven44099 thanks for reporting this issue. Release 1.8.4 to appera soon on pypi will fix the warning