[Bioperl-l] help:HMM parsing error

Jason Stajich jason at bioperl.org
Tue Sep 9 12:07:45 EDT 2008


Although it would be good to fix the parser as well --  best solution  
is to submit that report as a bug to bugzilla
http://bugzilla.open-bio.org/

-jason

On Sep 9, 2008, at 4:46 AM, Sendu Bala wrote:

> boyang zhe wrote:
>>  I write a script to parse the HMMER report ,it is as follows:
> [...]
>>   my $in = new Bio::SearchIO(-format => 'hmmer',-file =>"$infile");
> [...]
>>   -------------------- WARNING ---------------------
>>   MSG: unrecognized line:                      +E +L i T eek+ e+  + 
>> + +l++H
>>   Y+   I+ +
>>   ---------------------------------------------------
>>   why? I hope to get your help, hanks very much!
>
> I didn't check your code, but the easiest thing to try would be to  
> use -format => 'hmmer_pull' to use an alternate parser that may be  
> able to recognise that line. You might need to install the latest  
> Bioperl from SVN (or at least 1.5.2) to get access to the hmmer_pull  
> parser.
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Jason Stajich
jason at bioperl.org





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