[BioPython] Biopython BLAST parser error

[Jeffrey Chang]

Hello,

Which version of Biopython are you using?  The currect version of the 
parser in the CVS repository doesn't seem to do this anymore.  Try 
grabbing the latest Bio/Blast/NCBIStandalone.py file from 
cvs.biopython.org and see if that solves the problem.  Please let me 
know if it doesn't.

Jeff




On Monday, May 26, 2003, at 07:06  AM, m at pavis.biodec.com wrote:

> Hello
>     I've got a problem parsing the following output:
>
> http://pavis.biodec.com/~m/1be3_C.blast.bz2 (warning *big file*)
>
> It was written by
>
> blastpgp -d nr -e 1e-9 -b 10000 -v 10000 -j3
>
> on this protein: 1be3.pdb C.chain
>
> MTNIRKSHPLMKIVNNAFIDLPAPSNISSWWNFGSLLGICLILQILTGLFLAMHYTSDTTTA
> FSSVTHICRDVNYGWIIRYMHANGASMFFICLYMHVGRGLYYGSYTFLETWNIGVILLLTVM
> ATAFMGYVLPWGQMSFWGATVITNLLSAIPYIGTNLVEWIWGGFSVDKATLTRFFAFHFILP
> FIIMAIAMVHLLFLHETGSNNPTGISSDVDKIPFHPYYTIKDILGALLLILALMLLVLFAPD
> LLGDPDNYTPANPLNTPPHIKPEWYFLFAYAILRSIPNKLGGVLALAFSILILALIPLLHTS
> KQRSMMFRPLSQCLFWALVADLLTLTWIGGQPVEHPYITIGQLASVLYFLLILVLMPTAGTI
> ENKLLKW
>
> The Blast version that I am running is
>
> BLASTP 2.2.4 [Aug-26-2002]
>
> but I've got the same behaviour with BLASTP 2.1.3 [Apr-1-2001]
>
> I do not know the nr version number, but it is the databases
> with 705,002 sequences; 222,117,092 total letters (sorry for not
> having better information)
>
> As I see it, the problem lies in parsing the rows number 298999
> and number 588182, where the is the phrase:
>
> ``Sequences not found previously or not previously below threshold:''
>
> I am testing BioPython 1.10a, under Python 2.2.2, GNU / Linux /
> Debian Unstable
>
> p.s.: the trace of the error, apart from irrrelevant data, is
>
>     blast_parse=parser.parse(UndoHandle(blastfile))
>   File "/usr/lib/python2.2/site-packages/Bio/Blast/NCBIStandalone.py",
> line 611, in parse
>     self._scanner.feed(handle, self._consumer)
>   File "/usr/lib/python2.2/site-packages/Bio/Blast/NCBIStandalone.py",
> line 84, in feed
>     self._scan_rounds(uhandle, consumer)
>   File "/usr/lib/python2.2/site-packages/Bio/Blast/NCBIStandalone.py",
> line 139, in _scan_rounds
>     self._scan_descriptions(uhandle, consumer)
>   File "/usr/lib/python2.2/site-packages/Bio/Blast/NCBIStandalone.py",
> line 245, in _scan_descriptions
>     read_and_call_until(uhandle, consumer.description, blank=1)
>   File "/usr/lib/python2.2/site-packages/Bio/ParserSupport.py", line
> 371, in read_and_call_until
>     method(line)
>   File "/usr/lib/python2.2/site-packages/Bio/Blast/NCBIStandalone.py",
> line 677, in description
>     dh = self._parse(line)
>   File "/usr/lib/python2.2/site-packages/Bio/Blast/NCBIStandalone.py",
> line 734, in _parse
>     dh.score = _safe_int(dh.score)
>   File "/usr/lib/python2.2/site-packages/Bio/Blast/NCBIStandalone.py",
> line 1633, in _safe_int
>     return long(float(str))
> ValueError: invalid literal for float(): b
>
> -- 
>  .*.                            finelli
>  /V\
> (/ \) --------------------------------------------------------------
> (   )       Linux: Friends dont let friends use Piccolosoffice
> ^^-^^ --------------------------------------------------------------
>
> And the crowd was stilled.  One elderly man, wondering at the sudden 
> silence,
> turned to the Child and asked him to repeat what he had said.  
> Wide-eyed,
> the Child raised his voice and said once again, "Why, the Emperor has 
> no
> clothes!  He is naked!"
> - "The Emperor's New Clothes"
> _______________________________________________
> BioPython mailing list  -  BioPython at biopython.org
> http://biopython.org/mailman/listinfo/biopython