[Bioperl-l] [BULK] Re: can't parse blast file anymore

[Ryan Golhar]

I'm not sure how applicable this is, but I've seen a problem with Perl
if the LANG environment variable contain UTF8 (ex LANG=en_US.UTF8).
I've changed mine to en_US and lots of perl string parsing problems went
away.

Also, what about running the bioperl tests on your installation (make
test).  What happens?


-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org
[mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Chris Fields
Sent: Friday, May 05, 2006 3:18 PM
To: 'Hubert Prielinger'; 'Torsten Seemann'; bioperl-l at bioperl.org
Subject: Re: [Bioperl-l] [BULK] Re: can't parse blast file anymore


What happens if you add the verbose flag?

my $search = new Bio::SearchIO (-verbose => 1,
                                -format => 'blast',
                                -file => $file);

Added thought : you might want to look at File::Find for stepping
through your files and performing a task on each one, such as parsing
output.  It changes into the working directory each time; you should be
able to do something like this:

use File::Find;
use Bio::SearchIO;




Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- 
> bounces at lists.open-bio.org] On Behalf Of Hubert Prielinger
> Sent: Friday, May 05, 2006 1:30 PM
> To: Torsten Seemann; bioperl-l at bioperl.org
> Subject: Re: [Bioperl-l] [BULK] Re: can't parse blast file anymore
> 
> hi,
> I have done, as you suggested and I got the error message:
> 
> Can't call method "next_result" on an undefined value at....
> 
> then I looked up at the internet and found a thread which suggested to

> use strict and then the problem is solved.... but I'm already using 
> use strict..
> 
> thanks
> 
> Torsten Seemann wrote:
> > Hubert Prielinger wrote:
> >
> >> if I do so it returns:
> >> 0 undef
> >>
> >
> > That means the value of $search was undef.
> > That means that it could not parse or open the BLAST report. I 
> > repeat the line that I put in my earlier email which you ignored.
> >
> > # your line
> > my $search = Bio::SearchIO->new( ..... );
> >
> > # then check if it was successful!
> > die "could not open blast report" if not defined $search;
> >
> > --Torsten
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org 
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> >
> >
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org 
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