[BioPython] import Standalone problems

Rohini Damle rohini.damle at gmail.com
Thu Jul 20 19:05:14 UTC 2006 

Hi,
I used hsp.evalue instead of hsp.expect and I am getting the desired output.

Thank you very much for your help, efforts, and all those modified files.
Rohini

On 7/20/06, Rohini Damle <rohini.damle at gmail.com> wrote:
> Hi,
> Now I used your updated Record.py, NCBIXML.py and NcbiStandalone.py
> (all updated)
> I am not getting that previous error.
> BUT I am still not getting the desired output ...
> Here is my code
>
> blast_out = open("C:/Documents and Settings/rdamle/My
> Documents/Rohini's Documents/Blast
> Parsing/onlymouse4proteinblastout.xml", "r")
>
> b_parser = NCBIXML.BlastParser()
> b_iterator = NCBIStandalone.Iterator(blast_out, b_parser)
> E_VALUE_THRESH = 22
>
> for b_record in b_iterator :
>             for alignment in b_record.alignments:
>                    for hsp in alignment.hsps:
>                        if (hsp.expect< E_VALUE_THRESH):
>                                print b_record.query.split()[0]
>                                print '****Alignment****'
>                                print 'sequence:',
> alignment.title.split()[0]
>
>
> with this code I was expecting to get all the alignments with
> hsp.expect<E_VALUE_THRESH
>
> BUT I AM GETTING ALL the alignments not just the one with evalue <22
> -Rohini.
>
>
>
>
>
> On 7/20/06, Jacob Joseph <jmjoseph at andrew.cmu.edu> wrote:
> > Hi.  I suspect you are not using my updated Record.py.   You'll notice
> > that, at least for the moment, I have changed _blast.gap_penalties to an
> > array to allow assignment per item without worrying about the order of
> > entries within the xml file.  There are other ways this could be
> > accomplished while still using a tuple.
> >
> > -Jacob
> >
> > Rohini Damle wrote:
> > > 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
> > >>
> > >>
> > >>
> > >> _______________________________________________
> > >> BioPython mailing list  -  BioPython at lists.open-bio.org
> > >> http://lists.open-bio.org/mailman/listinfo/biopython
> > >>
> > >>
> > >>
> > >>
> > _______________________________________________
> > BioPython mailing list  -  BioPython at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biopython
> >
>

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