[Bioperl-l] Blast returns result, but does not return hits

Raghunath Verabelli iamvela at yahoo.com
Thu Feb 23 11:23:56 EST 2006


Thanks Chris for all your help.

The patch for blast.pm worked. I was able to parse the
hits from the raw file. I uninstalled previous
versions of bioperl using ppm and then I installed
bioperl 1.4.x using nmake, and applied your fix. I am
getting hits the way I wanted.

However, I noticed that the p-value for each hit
doesn't seem to be parsed
correctly. It sets it to 0 for all hits. Not sure if
this is a known issue. Any suggestions/comments,
please let me know.

Thanks,
Raghu

--- Chris Fields <cjfields at uiuc.edu> wrote:

> > -----Original Message-----
> > From: bioperl-l-bounces at lists.open-bio.org
> [mailto:bioperl-l-
> > bounces at lists.open-bio.org] On Behalf Of Raghunath
> Verabelli
> > Sent: Wednesday, February 22, 2006 8:25 PM
> > To: Chris Fields; bioperl-l at lists.open-bio.org
> > Subject: Re: [Bioperl-l] Blast returns result, but
> does not return hits
> > 
> > 
> > Thanks very much Chris for your time.
> > Please see below output that you requested (the
> only
> > difference i saw between your output and mine is
> @INC
> > value. I have only 2 directories c:\mod_perl\perl
> > where i installed activeperl. I see two additional
> > directories in your @INC path).
> > 
> > >
> > > When you type 'perl -V' what do you see (make
> sure
> > > it is a capital 'V', not
> > > lower case).
> > 
> > C:\Documents and Settings\Administrator>perl  -V
> > Summary of my perl5 (revision 5 version 8
> subversion
> > 7) configuration:
> >   Platform:
> >     osname=MSWin32, osvers=5.0,
> > archname=MSWin32-x86-multi-thread
> 
> [....]
> 
> > if.pm
> >   Built under MSWin32
> >   Compiled at Nov  2 2005 08:44:52
> >   %ENV:
> >     PERL5LIB="c:\bioperl-live"
> >   @INC:
> >     c:\bioperl-live
> >     C:/mod_perl/Perl/lib
> >     C:/mod_perl/Perl/site/lib
> >     .
> 
> Personally I wouldn't place the the bioperl-live
> folder in the root
> directory; this shouldn't make a difference, but you
> can try moving it to
> the perl directory in a separate folder to see if
> that helps.  Can't see why
> it would make a difference, but it is Windows...
> Main reason I'll switching
> over to Mac OS X!
> 
> Make sure that the Bio directory is in the
> bioperl-live directory,
> regardless (i.e. if PERL5LIB is set to
> C:\mod_perl\Perl\bioperl\bioperl-live, then there
> should be a directory like
> C:\Perl\bioperl\bioperl-live\Bio).  Otherwise it
> won't work.
> 
> What do you get with this?
> 
> perl -MBio::Root::Version -e "print
> $Bio::Root::Version::VERSION"
> 
> If everything is working (PERL5LIB, etc) then it
> should be 1.5 for CVS
> bioperl; otherwise it will either find the old
> version (1.2.3) or fail
> completely.
> 
> Christopher Fields
> Postdoctoral Researcher - Switzer Lab
> Dept. of Biochemistry
> University of Illinois Urbana-Champaign 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 


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