Well, some times we need to reinvent the wheel when things change. With the advent of NGS and other technologies in bioinformatics, we see many questions that were addressed a decade ago. Tools that existed earlier, do not exist any more. One of the requests I got was to extract KEGG pathway IDs and pathways using gene symbols. Let us do this in python using bioservices library. Bioservices is a python libraries for accessing web services from several bioinformatics servers. You can visit them here. Example genes are furnished along with the code. Examples are human genes. Probably i will add other genes (from prokaryotes) when I get another request. Let us do this with a very simple script. Install bioservices library from pypi, pip3, conda, system repos whichever you like. This script works with python 3.6 and bioservices 1.5.2 (as of today, June 6th, 2018).
code (make sure that indentation is correct. Python is very strict about indenting):
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> genes=["CRK","RUNX1","PSMD11","JUP"]
> print(genes)
['CRK', 'RUNX1', 'PSMD11', 'JUP']
> for i in genes:
j=k.get_pathway_by_gene(i,"hsa")
for keys,values in j.items():
print(i,keys, values, sep="\t")
RK hsa04010 MAPK signaling pathway
> print(genes)
['CRK', 'RUNX1', 'PSMD11', 'JUP']
> for i in genes:
j=k.get_pathway_by_gene(i,"hsa")
for keys,values in j.items():
print(i,keys, values, sep="\t")
RK hsa04010 MAPK signaling pathway
CRK hsa04012 ErbB signaling pathway
CRK hsa04015 Rap1 signaling pathway
CRK hsa04062 Chemokine signaling pathway
CRK hsa04510 Focal adhesion
CRK hsa04666 Fc gamma R-mediated phagocytosis
CRK hsa04722 Neurotrophin signaling pathway
CRK hsa04810 Regulation of actin cytoskeleton
CRK hsa04910 Insulin signaling pathway
CRK hsa05100 Bacterial invasion of epithelial cells
CRK hsa05131 Shigellosis
CRK hsa05200 Pathways in cancer
CRK hsa05206 MicroRNAs in cancer
CRK hsa05211 Renal cell carcinoma
CRK hsa05220 Chronic myeloid leukemia
RUNX1 hsa04530 Tight junction
RUNX1 hsa04659 Th17 cell differentiation
RUNX1 hsa05200 Pathways in cancer
RUNX1 hsa05202 Transcriptional misregulation in cancer
RUNX1 hsa05220 Chronic myeloid leukemia
RUNX1 hsa05221 Acute myeloid leukemia
PSMD11 hsa03050 Proteasome
PSMD11 hsa05169 Epstein-Barr virus infection
JUP hsa05200 Pathways in cancer
JUP hsa05202 Transcriptional misregulation in cancer
JUP hsa05221 Acute myeloid leukemia
JUP hsa05226 Gastric cancer
JUP hsa05412 Arrhythmogenic right ventricular cardiomyopathy (ARVC)
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