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

[Christopher Fields]

These are debugging lines (not errors); you still have the -verbose flag set.  

Did you follow Jason's advice?  I believe he's right on the money about the issue 
at hand...

Chris

---- Original message ----
>Date: Sun, 07 May 2006 19:41:14 -0600
>From: Hubert Prielinger <hubert.prielinger at gmx.at>  
>Subject: Re: [Bioperl-l] [BULK]  can't parse blast file anymore  
>To: Torsten Seemann <torsten.seemann at infotech.monash.edu.au>, bioperl-
l at bioperl.org, Chris Fields <cjfields at uiuc.edu>, Jason Stajich 
<jason.stajich at duke.edu>
>
>hi,
>I have corrected that and now I finally I got a few error messages:
>
>blast.pm: unrecognized line Reference: Altschul, Stephen F., Thomas L. 
>Madden, Alejandro A. Schäffer,
>blast.pm: unrecognized line Jinghui Zhang, Zheng Zhang, Webb Miller, and 
>David J. Lipman
>blast.pm: unrecognized line (1997), "Gapped BLAST and PSI-BLAST: a new 
>generation of
>blast.pm: unrecognized line protein database search programs", Nucleic 
>Acids Res. 25:3389-3402.
>blast.pm: unrecognized line RID: 
1137529800-24476-151611170370.BLASTQ1
>
>after that line it stops without terminating....
>
>
>Torsten Seemann wrote:
>> 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.
>>
>