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

Chris Fields cjfields at uiuc.edu
Thu Feb 23 12:41:07 EST 2006


Yes that's a potential issue.  I'll try to replicate that here; please send
a code example so I can see how you're calling for the p-value.

Christopher Fields
Postdoctoral Researcher - Switzer Lab
Dept. of Biochemistry
University of Illinois Urbana-Champaign 

> -----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: Thursday, February 23, 2006 10:24 AM
> To: Chris Fields; bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] Blast returns result, but does not return hits
> 
> 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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