[BioPython] Changes in NCBI BLAST output format
Martina
boehme at mpiib-berlin.mpg.de
Mon Sep 5 05:10:39 EDT 2005
Hello Michiel,
I got your fix for NCBIWWW.py from the CVS, but now I get a diffrent
error message: SyntaxError: Line does not contain 'Database':
.
.
.
File "C:\Python24\Lib\site-packages\Bio\Blast\NCBIWWW.py", line 47, in parse
self._scanner.feed(handle, self._consumer)
File "C:\Python24\Lib\site-packages\Bio\Blast\NCBIWWW.py", line 100, in feed
self._scan_header(uhandle, consumer)
File "C:\Python24\Lib\site-packages\Bio\Blast\NCBIWWW.py", line 172, in
_scan_header
self._scan_database_info(uhandle, consumer)
File "C:\Python24\Lib\site-packages\Bio\Blast\NCBIWWW.py", line 190, in
_scan_database_info
read_and_call(uhandle, consumer.database_info, contains='Database')
File "C:\Python24\Lib\site-packages\Bio\ParserSupport.py", line 301, in
read_and_call
raise SyntaxError, errmsg
This is the sequence I blasted: GGAAGATAATGAACACCAAGA
result_handle = NCBIWWW.qblast('blastn', 'nr', f_record, expect = 100,
word_size = 7,filter = 'L',entrez_query = 'Homo sapiens
[ORGN]',descriptions=10,alignments=50)
(I added word_size to qblast, but that doesn't make any difference)
I tried to workout what the problem was, but I don't find it that easy
to see, what it is the blast parser is exactly doing. I'm wondering why
nobody else seems to get this error? Thanks for any help!
Martina
More information about the BioPython
mailing list