[BioPython] Bioregistry...doesn't work with me

Aurélie Bornot aurelie.bornot at free.fr
Fri Apr 1 08:04:15 EST 2005


Hello,

Sorry for "spaming"

I am trying to retrieve sequences with the script of the CookBook and it doesn't work...
I don't understand why....
Can someone tell me what I did wrong ?

>>> from Bio import db
>>> print db
db, exporting 'embl', 'embl-dbfetch-cgi', 'embl-ebi-cgi', 'embl-fast', 'embl-xem
bl-cgi', 'embl-xml', 'fasta', 'fasta-sequence-eutils', 'genbank-nucleotide', 'ge
nbank-protein', 'interpro', 'interpro-ebi-cgi', 'medline', 'medline-eutils', 'nu
cleotide-genbank-eutils', 'pdb', 'pdb-ebi-cgi', 'pdb-rcsb-cgi', 'prodoc', 'prodo
c-expasy-cgi', 'prosite', 'prosite-expasy-cgi', 'protein-genbank-eutils', 'swiss
prot', 'swissprot-expasy-cgi', 'swissprot-usmirror-cgi'
>>> db.keys()
['embl-dbfetch-cgi', 'embl-xml', 'fasta', 'prodoc-expasy-cgi', 'interpro', 'pdb-
rcsb-cgi', 'swissprot-expasy-cgi', 'swissprot', 'prosite', 'swissprot-usmirror-c
gi', 'fasta-sequence-eutils', 'interpro-ebi-cgi', 'embl', 'nucleotide-genbank-eu
tils', 'protein-genbank-eutils', 'prodoc', 'prosite-expasy-cgi', 'embl-fast', 'm
edline', 'genbank-nucleotide', 'pdb-ebi-cgi', 'medline-eutils', 'genbank-protein
', 'embl-ebi-cgi', 'embl-xembl-cgi', 'pdb']
>>> sp = db["swissprot"]
>>> sp
<Bio.config.DBRegistry.DBGroup instance at 0x00ACEB48>
>>> record_handle = sp['O23729']
Traceback (most recent call last):
  File "<stdin>", line 1, in ?
  File "C:\Python24\lib\site-packages\Bio\config\DBRegistry.py", line 150, in __
getitem__
    data = self._run_serial(key)
  File "C:\Python24\lib\site-packages\Bio\config\DBRegistry.py", line 217, in _r
un_serial
    raise KeyError, "I could not get any results."
KeyError: 'I could not get any results.'


I have verified : the entry O23729 is still correct....
I must work with Windows XP, may the problem comes from this...?

Thanks !
Aurélie






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