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

[Chris Fields]

Sorry, mail got sent before I finished it!  Here I go again...

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;

my @dirlist = ("/home/Hubert/test");

find (\&dir, @dirlist);

sub printdir {
    return unless /txt$/; 
    return if (-d);
    my $parser = Bio::SearchIO->new(-file => $_,
                                    -format => 'blast');	
    while (my $result = $parser->next_result) {
        while (my $hit = $result->next_hit) {
            while (my $hsp = $hit->next_hsp) {
                # do stuff here
            }
        }
    }
}

Chris

> -----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
> >
> >
> >
> 
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