[Bioperl-l] FW: Issue with Bio::SearchIO::psl (was: Bioperl bug 1977)

[Chris Fields]

Of course I forgot to forward this...

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


Original message:


I'm going to go back on the mail list since it's probably not the script,
though it still sounds like an input file issue via IO::String.  Jason may
have some ideas on this as well.  

On the surface it looks like the end_document method isn't called for some
reason so it tries reading through, gets undef and chokes.  However I am
unable to replicate that here (everything ends as expected).  It doesn't
hurt to add your fix as a failsafe so I'll go ahead and commit it (it passes
all tests) but I would like you to try a few things first.

Did you try 'make test' when you installed bioperl from CVS?  I had
previously thought that the psl tests weren't included but they are actually
under UCSCParsers.t.  This error ("Use of uninitialized value in pattern
match (m//)") should pop up if you run 'make test'.  Or, even simpler, run
this from the bioperl-live directory (where you ran 'perl Makefile.PL, and
'make test'):

perl -I. -w t/USCSParsers.t

The only other thing I can think of is that, in your original test run of
the script, your error line indicated that you had a local installation of
bioperl and that version of Bio::SearchIO::psl was the one causing the
error:

Use of uninitialized value in pattern match (m//) at /Users/albert/
Documents/CSHL/cvswork/bioperl-live/Bio/SearchIO/psl.pm line 173, <GEN1>
line 10.

Is it possible that you have two versions of bioperl installed, one in the
/Library/Perl folder and the one being used above?  If you tried
uninstalling and reinstalling using 'perl Makefile.PL', 'make', 'make
install' then it will install in your system by default (though I believe
you have to use 'sudo' for that).  If PERL5LIB is set to your local perl
version, it will use that one first.

Personally, I don't think that's it though it's worth a shot.  I tried old
versions of SearchIO::psl from CVS and they all seemed to work just fine, so
I'm a bit mystified about this one since you get the same error on Linux and
Mac OS X, but I don't get it on either WinXP or Mac OS X (both using a CVS
copy of bioperl with PERL5LIB).  

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


> -----Original Message-----
> From: Albert Vernon Smith [mailto:smithav at cshl.edu]
> Sent: Tuesday, April 04, 2006 1:27 PM
> To: Chris Fields
> Subject: Re: [Bioperl-l] Issue with Bio::SearchIO::psl (was: Bioperl 
> bug
> 1977)
> 
> it is exactly your script where i get this (as well as my own 
> variations).  plus data for the test.
> 
> -a