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

[Hubert Prielinger]

hi all together,
i have solved the problem, because I'm parsing blast 2.2.13 and I have 
installed an early bioperl 1.5.1 and there it occurred that
bug 1934 wasn't fixed yet, so I had to exchange the blast.pm file and 
now it works properly.

thank you very much
Hubert

Christopher Fields wrote:
> 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.
>>>
>>>       
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
>