WARNING [bioservices:keggparser:119]
raven44099 opened this issue · comments
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.
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 <module>
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?
@raven44099 thanks for reporting this issue.
Release 1.8.4 to appera soon on pypi will fix the warning