[Bioperl-l] Parsing BLAST 2.2.14 output

Sendu Bala sb at mrc-dunn.cam.ac.uk
Thu Jun 15 15:00:38 EDT 2006


Susan J. Miller wrote:
> We are unable to parse BLAST 2.2.14 results from the NCBI website using 
> SearchIO.  I have updated Bio::SearchIO::blast.pm to what's in 
> bioperl-live, but when users download either plain text or HTML blast 
> outputs from the NCBI page, SearchIO cannot parse them.  This used to 
> work prior to BLAST 2.2.14.  Should I try installing the entire 
> bioperl-live distribution?  (We are running Solaris 8 and perl 5.8 if 
> that makes any difference.)

Parsing saved results from the website works fine here. Please be more 
specific in what you mean by 'unable to parse'. What error messages do 
you get? What exact code did you use to get those errors? Exactly what 
input data did you use? Exactly how did you generate that data?

Cheers,
Sendu.


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