[BioPython] Problem using efetch

Alex Coventry throwaway at MIT.EDU
Wed Feb 21 18:31:56 UTC 2007


Hi.  The following query results in an error message from NCBI:

>>> print client.search('''
NP_542420
ATRTC
''', db='protein').efetch(retmode='text', rettype='fasta').read()
... ... ... ... 
Error: Internal Error

I expected this query to return two sequences in fasta format.  The same
query seems to work without problems at
<http://www.ncbi.nlm.nih.gov/entrez/batchentrez.cgi>.

Searching for either query separately also seems to work.  E.g.:

>>> print client.search('''
ATRTC
''', db='protein').efetch(retmode='text',
rettype='fasta').read()
... ... ... >gi|71620|pir||ATRTC actin beta - rat
MDDDIAALVVDNGSAMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYP
IEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQIMFETFNTPAMYVAIQAVL
SLYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGYSFTTTAEREIVR
DIKEKLCYVALDFEQEMATAASSSSLEKSYELPDGQVITIGNERFRCPEALFQPSFLGMESCGIHETTFN
SIMKCDVDIRKDLYANTVLSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLS
TFQQMWISKQEYDESGPSIVHRKCF

Am I doing something wrong, here?

Alex



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