[Bioperl-l] Re: [Bioperl-guts-l] Notification: incoming/937

[Jason Stajich]

Rex - I suspect this is a problem in the BPlite documentation, but without
any code I can't do much for you.

The documentation problem (which I have already fixed since the 07
release) is in the example code snippet from the top of the documentation
ie:

 use Bio::Tools::BPlite;
 my $report = new BPlite(-fh=>\*STDIN);

 {
 $report->query;
 $report->database;
 while(my $sbjct = $report->nextSbjct) {
     $sbjct->name;
     while (my $hsp = $sbjct->nextHSP) {
         $hsp->score;
         $hsp->bits;
         etc...

which is wrong.
It should read:
 use Bio::Tools::BPlite;
 my $report = new Bio::Tools::BPlite(-fh=>\*STDIN);

 {
 $report->query;
 $report->database;
 while(my $sbjct = $report->nextSbjct) {
     $sbjct->name;
     while (my $hsp = $sbjct->nextHSP) {
         $hsp->score;
         $hsp->bits;
         etc...

Please make sure that you are correctly calling the new method with the
correct package name (Bio::Tools::BPlite) and let us know if you are still
unable to make it work.

On Fri, 30 Mar 2001 bioperl-bugs@bioperl.org wrote:

> JitterBug notification
>
> new message incoming/937
>
> Message summary for PR#937
> 	From: tarpeyr@basf.com
> 	Subject: bplite 'Can't locate object method "new"
> 	Date: Fri, 30 Mar 2001 14:23:32 -0500
> 	0 replies 	0 followups
>
> ====> ORIGINAL MESSAGE FOLLOWS <====
>
> >From tarpeyr@basf.com Fri Mar 30 14:23:33 2001
> Received: from localhost (localhost [127.0.0.1])
> 	by pw600a.bioperl.org (8.11.2/8.11.2) with ESMTP id f2UJNW207856
> 	for <bioperl-bugs@pw600a.bioperl.org>; Fri, 30 Mar 2001 14:23:32 -0500
> Date: Fri, 30 Mar 2001 14:23:32 -0500
> Message-Id: <200103301923.f2UJNW207856@pw600a.bioperl.org>
> From: tarpeyr@basf.com
> To: bioperl-bugs@bioperl.org
> Subject: bplite 'Can't locate object method "new"
>
> Full_Name: Rex Tarpey
> Module: bplite
> Version: 0.7
> PerlVer: 5.6.0
> OS: irix
> Submission from: basfegw.basf-corp.com (144.29.1.2)
>
>
> I think this is more an install problem, but trying to utilize BPlite.pm gives
> the error message "Can't locat object method "new" via package "BPlite" at
> 'scipt nam line n'
> Other bioperl modules appear to work just fine (standaloneblast, seqIO, Index,
> etc)
>
>
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>

Jason Stajich
jason@chg.mc.duke.edu
Center for Human Genetics
Duke University Medical Center
http://www.chg.duke.edu/