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

[Hubert Prielinger]

hi ryan,
nothing happend if I add the verbose flag
and how can I test my bioperl installation.....


Ryan Golhar wrote:
> I'm not sure how applicable this is, but I've seen a problem with Perl
> if the LANG environment variable contain UTF8 (ex LANG=en_US.UTF8).
> I've changed mine to en_US and lots of perl string parsing problems went
> away.
>
> Also, what about running the bioperl tests on your installation (make
> test).  What happens?
>
>
> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org
> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Chris Fields
> Sent: Friday, May 05, 2006 3:18 PM
> To: 'Hubert Prielinger'; 'Torsten Seemann'; bioperl-l at bioperl.org
> Subject: Re: [Bioperl-l] [BULK] Re: can't parse blast file anymore
>
>
> 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;
>
>
>
>
> 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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>>     
>
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