[Bioperl-l] Bio::SearchIO blast_parsing

[Ralf Schmid]

Jason,

see attached, 

> ralf - can you send an example report - if I use your code and the
> t/data/ecolitst.bls report in the bioperl disto I get this
> jason at jason $ perl ralf_bug.pl
> AAC73113.1
> AAC73113.1
> AAC73113.1
> AAC73113.1

Just tried it for ecolitst.bls - it works fine ... 

 
> also see below.
> 
> -j


> This was a requested feature.  
makes perfectly sense (ie not having to fill up your disk with alignments if you
just want to extract hit and e-value)  

You can add a little code which exists the
> hit loop if the hit doesn't have any hsps
> last if $hit->num_hsps == 0;
> 

Thanks, 


Ralf


------------------------------------------------------------------------------- 

Dr. Ralf Schmid
Nematode Bioinformatics
Blaxter Nematode Genomics Group
Institute of Cell, Animal and Population Biology
Ashworth Labs						
University of Edinburgh				
King\'s Buildings					
Edinburgh			
EH9 3JT	 			
UK					

(+44)(0)131 650 7403


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