[Bioperl-l] Fwd: Help with BPLite

[Barry Moore]

Jianying-

There may be better ways, but you can check the version with perl
-MBio::Root::Version -e 'print "$Bio::Root::Version::VERSION\n"'.  Do
you want to send the Blast report that you are having trouble parsing
and I'll try it?

Barry

-----Original Message-----
From: Li, Jianying (NIH/NIEHS) [mailto:li11 at niehs.nih.gov] 
Sent: Friday, October 07, 2005 2:09 PM
To: Barry Moore
Subject: RE: [Bioperl-l] Fwd: Help with BPLite

Thank you for your attention!

I am using Windows XP, but I am not sure about my bioperl version. How
can I
test this? I used PPM to install bioperl: PPM install Bioperl, but never
test version.

The error message is pretty general, exactly like this:

------------------WARNING---------------------------
MSG: Possible error (1) while parsing BLAST report!
----------------------------------------------------

Thanks. 


Jianying Li
Bioinformatics Scientist
NIEHS ITSS Contractor
NIEHS MicroArray Center
111 Alexander Drive, Rm. C250
P.O. Box 12233
Research Triangle Park, NC 27709
VM:919-316-4612 Fax: 919-541-1506
li11 at niehs.nih.gov
http://www.niehs.nih.gov
http://dir.niehs.nih.gov/microarray




-----Original Message-----
From: Barry Moore [mailto:bmoore at genetics.utah.edu] 
Sent: Friday, October 07, 2005 4:02 PM
To: Jason Stajich; Bioperl list
Cc: Li, Jianying (NIH/NIEHS)
Subject: RE: [Bioperl-l] Fwd: Help with BPLite

Jianying-

Your script works fine for me on Windows XP, bioperl 1.4.  Give us some
details about your problem.  What errors are you getting?  What version
of
bioperl are you using.



-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org] On Behalf Of Jason
Stajich
Sent: Friday, October 07, 2005 12:53 PM
To: Bioperl list
Cc: li11 at niehs.nih.gov
Subject: [Bioperl-l] Fwd: Help with BPLite



Begin forwarded message:

> From: "Li, Jianying (NIH/NIEHS)" <li11 at niehs.nih.gov>
> Date: October 7, 2005 1:58:20 PM EDT
> Subject: Help with BPLite
>
>
> Dear all,
>
> I am trying to use BPLite package from BioPerl on a windows machine, 
> and got a warning message.
>
> Here is the sample code from BioPerl doc:
>
> use Bio::Tools::BPlite;
> open (FH, "blastResult.txt") || die "Can't open file for input.\n"; my

> $report = new Bio::Tools::BPlite(-fh=>\*FH); {
>      while(my $sbjct = $report->nextSbjct) {
>                   print ">",$sbjct->name,"\n";
>                   while(my $hsp = $sbjct->nextHSP) {
>                                    print "\t",$hsp->start,"..",$hsp-
> >end," ",$hsp->bits,"\n";
>                   }
>      }
> }
> exit 0;
>
> Then I tried run it on a Linux machine, and it worked.
>
> Could you please provide me some information how I can do it properly 
> in Windows system?
>
> Your any attention is appreciated.
>
> Jianying Li
> Bioinformatics Scientist
> NIEHS ITSS Contractor
> NIEHS MicroArray Center
> 111 Alexander Drive, Rm. C250
> P.O. Box 12233
> Research Triangle Park, NC 27709
> VM:919-316-4612 Fax: 919-541-1506
> li11 at niehs.nih.gov
> http://www.niehs.nih.gov
> http://dir.niehs.nih.gov/microarray
>
>
>
>

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