[Biopython] problem blasting on line
Jessica Grant
jgrant at smith.edu
Wed Nov 17 21:22:08 UTC 2010
Hello,
I am trying to use blast to extract contaminating sequences from a
set of 454 sequence data. My script uses NCBIWWW.qblast as follows:
result_handle = NCBIWWW.qblast("blastx", "nr",
record.format("fasta"), ncbi_gi=False, descriptions= "1",
alignments="1", format_type="XML", hitlist_size="1",
entrez_query='(Bacteria[ORGN])')
It works...for a while but it stops, eventually, with the following error:
raceback (most recent call last):
File "compBACTEUK.py", line 81, in <module>
main()
File "compBACTEUK.py", line 70, in main
blastBACTEUK(arg)
File "compBACTEUK.py", line 19, in blastBACTEUK
result_handleE = NCBIWWW.qblast("blastx", "nr",
record.format("fasta"), ncbi_gi=False, descriptions= "1",
alignments="1", format_type="XML", hitlist_size="1",
entrez_query='(Eukaryota[ORGN])')
File
"/Users/katzlab/Downloads/biopython-biopython-74d3c2a/build/lib.macosx-10.5-i386-2.5/Bio/Blast/NCBIWWW.py",
line 114, in qblast
handle = urllib2.urlopen(request)
File
"/System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/urllib2.py",
line 121, in urlopen
return _opener.open(url, data)
File
"/System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/urllib2.py",
line 380, in open
response = meth(req, response)
File
"/System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/urllib2.py",
line 491, in http_response
'http', request, response, code, msg, hdrs)
File
"/System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/urllib2.py",
line 418, in error
return self._call_chain(*args)
File
"/System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/urllib2.py",
line 353, in _call_chain
result = func(*args)
File
"/System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/urllib2.py",
line 499, in http_error_default
raise HTTPError(req.get_full_url(), code, msg, hdrs, fp)
urllib2.HTTPError: HTTP Error 404: Not Found
I suppose that the problem is a communication problem with ncbi. I
have written a try except statement into my script, but I seem to be
losing quite a few records as they get skipped over if the error
occurs.
I thought about downloading nr and using the standalone blast, but it
seems the downloadable nr database comes in several parts, already
formatted for blast. Can I concatenate these?
Any thoughts on the problem with the qblast or other ways to
circumvent this problem would be greatly appreciated!
Jessica
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