[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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