[BioPython] import Standalone problems

[Rohini Damle]

Hi,
When I tried on your NCBIXML.py code instead of oringinal one I am
getting following error messege:

File "C:\Python24\lib\site-packages\Bio\Blast\NCBIXML.py", line 210,
in _end_Parameters_gap_open
    self._blast.gap_penalties[0] = int(self._value)
TypeError: object does not support item assignment

in the original version
we don't have that " [0] " in self._blast.gap_penalties

what might be causing this error?
-Rohini

On 7/19/06, Jacob Joseph <jmjoseph at andrew.cmu.edu> wrote:
> I do not believe the current version of the parser will work with
> multiple queries using recent version of blast, regardless of the output
> format.  I do know that blastall 2.2.13 with XML functions with the
> parser corrections previously attached.  I have attached a further
> updated NCBIXML.py, fixing the performance issues in parse() that I
> mentioned.
>
> -Jacob
>
> Rohini Damle wrote:
> > Hi,
> > Can someone suggest me for which version of Blast, the Biopython's
> > (text or xml) parser works fine?
> > I will download that blast version locally and can use biopython's parser.
> > thanx,
> > Rohini
> >
> > On 7/18/06, Jacob Joseph <jacob at jjoseph.org> wrote:
> >> Hi.
> >> I encountered similar difficulties over the past few days myself and
> >> have made some improvements to the XML parser.  Well, that is, it now
> >> functions with blastall, but I have made no effort to parse the other
> >> blast programs.  I do not expect I have done any harm to other parsing,
> >> however.
> >>
> >> Attached are Record.py, NCBIStandalone.py, and NCBIXML.py.  I have not
> >> yet spent significant time to clean up my changes.  Without getting into
> >> specific modifications, I have made an effort to make consistent the
> >> variables in Record and NCBIXML, focusing primarily on what I needed
> >> this week.
> >>
> >> One portion I am not settled on reinitialization of Record.Blast at
> >> every call to iterator.next(), and, by extension, BlastParser.parse().
> >> See NCBIXML.py, line 114.  Without re-initializing this class, we run
> >> the risk of retaining portions of a Record from previously parsed
> >> queries.   This causes the bug 1970, mentioned below.  Unfortunately,
> >> this re-initialization exacts a significant performance penalty of at
> >> least a factor of 10 by some rough measures.  I would appreciate any
> >> suggestions for improvement here.
> >>
> >> I do apologize for not being more specific about my changes.  When I get
> >> a chance(next week?), I will package them up as a proper patch and file
> >> a bug.  Perhaps what I have done so far will be of use until then.
> >>
> >> fyi, I have done all of my testing with Blast 2.2.13.  2.2.14 seems to
> >> not have separate <?xml> blocks within its output, requiring a different
> >> method of iteration.
> >>
> >> -Jacob
> >>
> >> Peter wrote:
> >> > Rohini Damle wrote:
> >> >> Hi,
> >> >> I have a XML file with 4 blast records (for proteins P1, P2, P3, P4)
> >> >> I am trying to extract alignment information for each of them.
> >> >> So I wrote the following code:
> >> >>
> >> >>  for b_record in b_iterator :
> >> >>
> >> >>                 E_VALUE_THRESH =20
> >> >>                 for alignment in b_record.alignments:
> >> >>                        for hsp in alignment.hsps:
> >> >>                        if hsp.expect< E_VALUE_THRESH:
> >> >>
> >> >>                             print '****Alignment****'
> >> >>                             print 'sequence:',
> >> alignment.title.split()[0]
> >> >>
> >> >> With this code, I am getting information for P1,
> >> >> then information for P1 + P2
> >> >> then for P1+P2 +P3
> >> >> and finally for P1+P2+P3+P4
> >> >> why this is so?
> >> >> is there something wrong with the looping?
> >> >
> >> > I'm aware of something funny with the XML parsing, Bug 1970, which
> >> might
> >> > well be the same issue:
> >> >
> >> > http://bugzilla.open-bio.org/show_bug.cgi?id=1970
> >> >
> >> > I confess I haven't looked into exactly what is going wrong here - too
> >> > many other demands on my time to learn about XML and how BioPython
> >> > parses it.
> >> >
> >> > Does the work around on the bug report help?  Depending on which
> >> version
> >> > of standalone blast you have installed, you might have better luck with
> >> > plain text output - the trouble is this is a moving target and the NBCI
> >> > keeps tweaking it.
> >> >
> >> > Peter
> >> >
> >> > _______________________________________________
> >> > BioPython mailing list  -  BioPython at lists.open-bio.org
> >> > http://lists.open-bio.org/mailman/listinfo/biopython
>
>
>
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