[Bioperl-l] BLASTX parsing

Paulo Almeida paulo.david at netvisao.pt
Mon May 31 10:13:23 EDT 2004


You probably have a line in your script that is something like:

while (my $hit = $result->next_hit){

If you use 'if' instead of 'while', you only get the first hit. HSPs 
work the same way.
Other people will know how to answer your second question better, but I 
think SearchIO probably works with plain text, not html.

-Paulo Almeida

Javier Terol wrote:

> Hi,
> Thank you very much to all the people who helped me with my question 
> about parsing blast files.
> Following the advises I am working with the example perl script in the 
> Bio::SearchIO HOWTO. I have been working with this script and now I 
> can get easily de information I need.
> Now I would like only to get the data from the best hit for each 
> query, and not from all the ones obtained in the blast search (I 
> usually get 50 hits and 20 malignments). Can I do it modifying the 
> perl script I am working with? Could you help me o this?
> On te other hand, do the SearchIO modules work with htm files? I f it 
> is not tha case, is it ppossible to transform htm files to txt?
> Thank you very much in advance for your help
> Javier

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