[Biopython] Searching for and downloading sequences using the history

Carlos Javier Borroto carlos.borroto at gmail.com
Fri Sep 18 16:59:58 UTC 2009


Hi all,

I'm trying to download all of the EST from a specie, I'm following the
example on the tutorial which seems to be exactly what I need. But I
running into this problem:

>>> from Bio import Entrez
>>> Entrez.email = "carlos.borroto at gmail.com"
>>> dbname = "nucest"
>>> query_term = "Genus specie"
>>> search_handle = Entrez.esearch(db=dbname,term=query_term,usehistory="y")
>>> search_results = Entrez.read(search_handle)
>>> search_handle.close()
>>> len(search_results["IdList"])
20
>>> print search_results["Count"]
193951

So the assert statement if failing:
>>> gi_list = search_results["IdList"]
>>> count = int(search_results["Count"])
>>> assert count == len(gi_list)
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
AssertionError

And most important I'm not getting all of the ids.

Did someone knows what I'm doing wrong?

thanks in advance
-- 
Carlos Javier Borroto
Baltimore, MD
Phone: (410) 929 4020



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