[Bioperl-l] help:HMM parsing error

Sendu Bala bix at sendu.me.uk
Tue Sep 9 07:46:39 EDT 2008


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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