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

[Torsten Seemann]

Hubert Prielinger wrote:
> ok, thanks
> I have submitted the bug
> bug #1994

This is a line from the script you sent to Bugzilla:

my $search = new Bio::SearchIO (
-verbose => 1,-format => 'blast', -file => $file)
or die "could not open blast report" if not defined my $search;

Althoygh syntactically correct, I don't think it is doing what you want.
Please change it to this:

my $search = new Bio::SearchIO(-format => 'blast', -file => $file) or die 
"could not open blast report";

or alternatively, this:

my $search = new Bio::SearchIO(-format => 'blast', -file => $file);
if (not defined $search) {
   die "could not open blast report";
}

and let us know what happens.

all the example output you have supplied still suggests that Bio::SearchIO can 
not load or parse your blast report.

-- 
Torsten Seemann
Victorian Bioinformatics Consortium, Monash University, Australia