[BioPython] SyntaxError in NCBIWWW.BlastParser
Iddo Friedberg
idoerg at burnham.org
Tue Jun 22 11:57:01 EDT 2004
Definitely a bug. I think you are the second to report this. I'll have a
look.
Good catch. Sorry about that.
Iddo
Steven Walter wrote:
> Iddo wrote:
>
>> Steven Richard Walter wrote:
>>
>>> I'm getting a syntax error when parsing the results from a WWW blast
>>> query. Is this a bug in the BioPython code, or am I doing something
>>> stupid? In either case, hints on how to track down the problem will
>>> be greatly appreciated.
>>>
>>>
>>>
>> Kinda hard to do that without a bit more information.
>>
>> Can you please post the biopython version, Python version, OS you are
>> using, the sequence file, and (very important) the Python stack dump?
>>
>> Thanks,
>>
>> Iddo
>>
> Sorry about that. Python version 2.2.3, latest release of biopython on
> Linux (Fedora Core 2). Sequence is below the stack trace, run against
> the nr database with blastn. Hope that helps, and thanks for your reply
>
> >>> file = open("results")
> >>> from Bio.Blast import NCBIWWW
> >>> parser = NCBIWWW.BlastParser()
> >>> parser.parse(file)
> Traceback (most recent call last):
> File "<stdin>", line 1, in ?
> File "/usr/lib/python2.2/site-packages/Bio/Blast/NCBIWWW.py", line 47,
> in parse
> self._scanner.feed(handle, self._consumer)
> File "/usr/lib/python2.2/site-packages/Bio/Blast/NCBIWWW.py", line 99,
> in feed self._scan_rounds(uhandle, consumer)
> File "/usr/lib/python2.2/site-packages/Bio/Blast/NCBIWWW.py", line 242,
> in _scan_rounds
> self._scan_alignments(uhandle, consumer)
> File "/usr/lib/python2.2/site-packages/Bio/Blast/NCBIWWW.py", line 325,
> in _scan_alignments
> self._scan_pairwise_alignments(uhandle, consumer)
> File "/usr/lib/python2.2/site-packages/Bio/Blast/NCBIWWW.py", line 348,
> in _scan_pairwise_alignments
> self._scan_one_pairwise_alignment(uhandle, consumer)
> File "/usr/lib/python2.2/site-packages/Bio/Blast/NCBIWWW.py", line 379,
> in _scan_one_pairwise_alignment
> self._scan_alignment_header(uhandle, consumer)
> File "/usr/lib/python2.2/site-packages/Bio/Blast/NCBIWWW.py", line 417,
> in _scan_alignment_header
> raise SyntaxError, "I missed the Length in an alignment header"
> SyntaxError: I missed the Length in an alignment header
> >>>
>
> gcagcccagccaagcactgtcaggaatcctgtgaagcagctccagctatgtgtgaagaag
> aggacagcactgccttggtgtgtgacaatggctctgggctctgtaaggccggctttgctg
> gggacgatgctcccagggctgttttcccatccattgtgggacgtcccagacatcaggggg
> tgatggtgggaatgggacaaaaagacagctacgtgggtgacgaagcacagagcaaaagag
> gaatcctgaccctgaagtacccgatagaacatggcatcatcaccaactgggacgacatgg
> aaaagatctggcaccactctttctacaatgagcttcgtgttgcccctgaagagcatccca
> ccctgctcacggaggcacccctgaaccccaaggccaaccgggagaaaatgactcaaatta
> tgtttgagactttcaatgtcccagccatgtatgtggctatccaggcggtgctgtctctct
> atgcctctggacgcacaactggcatcgtgctggactctggagatggtgtcacccacaatg
> tccccatctatgagggctatgccttgccccatgccatcatgcgtctggatctggctggcc
> gagatctcactgactacctcatgaagatcctgactgagcgtggctattccttcgttacta
> ctgctgagcgtgagattgtccgggacatcaaggagaaactgtgttatgtagctctggact
> ttgaaaatgagatggccactgccgcatcctcatcctcccttgagaagagttacgagttgc
> ctgatgggcaagtgatcaccatcggaaatgaacgtttccgctgcccagagaccctgttcc
> agccatccttcatcgggatggagtctgctggcatccatgaaaccacctacaacagcatca
> tgaagtgtgatattgacatcaggaaggacctctatgctaacaatgtcctatcagggggca
> ccactatgtaccctggcattgccgaccgaatgcagaaggagatcacggccctagcaccca
> gcaccatgaagatcaagatcattgcccctccggagcgcaaatactctgtctggatcggtg
> gctccatcctggcctctctgtccaccttccagcagatgtggatcagcaaacaggaatacg
> atgaagccgggccttccattgtccaccgcaaatgcttctaaaacactttcctgctcctct
> ctgtctctagcacacaactgtgaatgtcctgtggaattatgccttcagttcttttccaaa
> tcattcctagccaaagctctgactcgttacctatgtgttttttaataaatctgaaatagg
> ctactggtaa
>
--
Iddo Friedberg, Ph.D.
The Burnham Institute
10901 N. Torrey Pines Rd.
La Jolla, CA 92037
USA
Tel: +1 (858) 646 3100 x3516
Fax: +1 (858) 713 9930
http://ffas.ljcrf.edu/~iddo
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