[Bioperl-l] Bio::Index::Abstract improvement

Emmanuel Quevillon emmanuel.quevillon at versailles.inra.fr
Tue Mar 20 16:36:18 EDT 2007


Dear list,

I started playing with Bio::Index::* module and particularly with 
Bio::Index::Blast.
But unfortunately, I have a problem with 
Bio::Index::Abstract::index_file method.

The thing is that when it indexes the input file, it forces the indexed 
file to have a key with the absolute path of the
original file to be indexed by using File::Spec::rel2abs.

What I would like to do is to index the file(s) in some place, on a 
faster machine than mine, and transfer
the original and indexed files onto mine to take profit of the index to 
retrieve results. Unfortunately, it is
not possible right now.
So I wondered if it could be possible to implement some kind of option 
to pass to the new
method to tell not to keep the absolute path of data file and then 
consider relative one.

I don't know if my request could interest more people, but I think this 
could be interesting anyway.
 
Thanks in advance

Regards

Emmanuel



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