[BioPython] FASTA parsing errors
Jeffrey Chang
jeffrey_chang at stanfordalumni.org
Tue Aug 3 16:23:33 EDT 2004
Hi Aaron,
Can you send the file that is generating the error? I believe it is
called /var/www/html/data/a12345.fasta. In general, the fasta parser
should be well-tested. It works on a test file in fasta format that I
have here. It would help most if someone could look at your file to
see what's going on.
Thanks,
Jeff
On Aug 3, 2004, at 3:42 PM, Aaron Zschau wrote:
> I've sent a couple messages to the list about this but I'm not sure if
> they're going through as I haven't seen any replies. I am trying to
> get a section of my code that worked before the 1.30 revision of
> biopython, based on the cookbook tutorials. My code looks up a gene by
> name in genbank and saves the FASTA version of that data so that the
> protein string can be fed into a BLAST search. The lookup works fine
> and I get a FASTA file saved just fine, however I then get an error at
> the parse stage at character 0 of the file.
>
> Any help would be greatly appreciated
>
> thanks
>
> Aaron Zschau
>
>
>
>
>
>
> #file_for_blast = open(data_path_prefix + file_unique_id + 'fasta',
> 'r')
> file_for_blast = open('/var/www/html/data/a12345.fasta','r')
>
> f_iterator = Fasta.Iterator(file_for_blast)
> print "iterator created"
> sys.stdout.flush()
>
> f_record = f_iterator.next()
> print "f_record created"
> sys.stdout.flush()
>
> -----------------------
>
> iterator created
> Traceback (most recent call last):
> File "cluster-debug.py", line 119, in ?
> f_record = f_iterator.next()
> File
> "/root/biopython-1.30/build/lib.linux-i586-2.2/Bio/Fasta/__init__.py",
> line 72, in next
> result = self._iterator.next()
> File
> "/root/biopython-1.30/build/lib.linux-i586-2.2/Martel/IterParser.py",
> line 152, in iterateFile
> self.header_parser.parseString(rec)
> File
> "/root/biopython-1.30/build/lib.linux-i586-2.2/Martel/Parser.py", line
> 361, in parseString
> self._err_handler.fatalError(ParserIncompleteException(pos))
> File "/usr/lib/python2.2/site-packages/_xmlplus/sax/handler.py",
> line 38, in fatalError
> raise exception
> Martel.Parser.ParserIncompleteException: error parsing at or beyond
> character 0 (unparsed text remains)
>
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