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

[Christopher Fields]

The -verbose flag was my suggestion; it should output a ton of debugging info 
from SearchIO::blast; if you see anything there, then it means that it's at least 
attempting to parse the report.  

Of course I can't test this myself at the moment since my wife's computer died 
(along with the bioperl setup); I'm using a loaner computer at the moment.

Chris

---- Original message ----
>Date: Sun, 07 May 2006 10:57:14 +1000
>From: Torsten Seemann <torsten.seemann at infotech.monash.edu.au>  
>Subject: Re: [Bioperl-l] [BULK]  can't parse blast file anymore  
>To: Hubert Prielinger <hubert.prielinger at gmx.at>
>Cc: bioperl-l at bioperl.org
>
>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
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