[Bioperl-l] Blast returns result, but does not return hits
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.
--- Chris Fields <cjfields at uiuc.edu> wrote:
> > -----Original Message-----
> > From: bioperl-l-bounces at lists.open-bio.org
> > bounces at lists.open-bio.org] On Behalf Of Raghunath
> > 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
> > difference i saw between your output and mine is
> > 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
> > > it is a capital 'V', not
> > > lower case).
> > C:\Documents and Settings\Administrator>perl -V
> > Summary of my perl5 (revision 5 version 8
> > 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
> 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
> 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
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