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Sep 4th, 2015
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  1. from Bio import Entrez
  2. from itertools import islice
  3.  
  4. Entrez.email = "bintriz@gmail.com"
  5.  
  6. q_result = Entrez.read(Entrez.elink(db="gene", dbfrom="cdd", id="276006"))
  7. ig_geneids = [ link["Id"] for link in q_result[0]["LinkSetDb"][0]["Link"] ]
  8.  
  9. def build_geneid_query(geneids, size):
  10. it = iter(geneids)
  11. q = ','.join(list(islice(it, size)))
  12. while q:
  13. yield q
  14. q = ','.join(list(islice(it,size)))
  15.  
  16. ig_genes = []
  17. for q in build_geneid_query(ig_geneids, 100):
  18. q_result = Entrez.read(Entrez.esummary(db="gene", id=q))
  19. ig_genes += q_result["DocumentSummarySet"]["DocumentSummary"]
  20.  
  21. ig_genes_human = [ gene for gene in ig_genes if gene["Organism"]["CommonName"] == "human" ]
  22.  
  23. for gene in reversed(ig_genes_human):
  24. geneid = gene.attributes["uid"]
  25. name = gene["Name"]
  26. desc = gene["Description"]
  27. print("%s\t%s\t%s" % (geneid, name, desc))
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