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- from Bio import Entrez
- from itertools import islice
- Entrez.email = "bintriz@gmail.com"
- q_result = Entrez.read(Entrez.elink(db="gene", dbfrom="cdd", id="276006"))
- ig_geneids = [ link["Id"] for link in q_result[0]["LinkSetDb"][0]["Link"] ]
- def build_geneid_query(geneids, size):
- it = iter(geneids)
- q = ','.join(list(islice(it, size)))
- while q:
- yield q
- q = ','.join(list(islice(it,size)))
- ig_genes = []
- for q in build_geneid_query(ig_geneids, 100):
- q_result = Entrez.read(Entrez.esummary(db="gene", id=q))
- ig_genes += q_result["DocumentSummarySet"]["DocumentSummary"]
- ig_genes_human = [ gene for gene in ig_genes if gene["Organism"]["CommonName"] == "human" ]
- for gene in reversed(ig_genes_human):
- geneid = gene.attributes["uid"]
- name = gene["Name"]
- desc = gene["Description"]
- print("%s\t%s\t%s" % (geneid, name, desc))
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