runchuan-bu/bioclaw/query-kegg

import requests
BASE_URL = "https://rest.kegg.jp"
# 1. Find pathways by keyword
def find_pathways(keyword, organism="hsa"):
    url = f"{BASE_URL}/find/pathway/{keyword}"
    r = requests.get(url)
    lines = r.text.strip().split('\n')
    results = []
    for line in lines:
        if line:
            parts = line.split('\t')
            pid = parts[0].replace("map", organism) if organism else parts[0]
            results.append({"id": pid, "name": parts[1] if len(parts) > 1 else ""})
    return results
# 2. Get pathway details
def get_pathway(pathway_id):
    url = f"{BASE_URL}/get/{pathway_id}"
    r = requests.get(url)
    return r.text
# 3. Get genes in a pathway
def get_pathway_genes(pathway_id):
    url = f"{BASE_URL}/link/genes/{pathway_id}"
    r = requests.get(url)
    genes = []
    for line in r.text.strip().split('\n'):
        if line:
            parts = line.split('\t')
            if len(parts) >= 2:
                genes.append(parts[1])
    return genes
# 4. Get gene info
def get_gene(kegg_gene_id):
    url = f"{BASE_URL}/get/{kegg_gene_id}"
    r = requests.get(url)
    return r.text
# 5. Find genes by name
def find_gene(gene_name, organism="hsa"):
    url = f"{BASE_URL}/find/{organism}/{gene_name}"
    r = requests.get(url)
    return r.text
# 6. List all human pathways
def list_pathways(organism="hsa"):
    url = f"{BASE_URL}/list/pathway/{organism}"
    r = requests.get(url)
    return r.text
# Example
pathways = find_pathways("apoptosis")
for p in pathways[:5]:
    print(f"{p['id']}: {p['name']}")