[Bioperl-l] Bio::SearchIO blast_parsing

Ralf Schmid R.Schmid at ed.ac.uk
Wed Mar 17 16:42:47 EST 2004


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;




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

(+44)(0)131 650 7403

-------------- next part --------------
A non-text attachment was scrubbed...
Name: test.out
Type: application/octet-stream
Size: 16977 bytes
Desc: not available
Url : http://portal.open-bio.org/pipermail/bioperl-l/attachments/20040317/e077f2a1/test.obj

More information about the Bioperl-l mailing list