[Bioperl-l] Bio::DB::Fasta errors

[Venky Nandagopal]

I've been noticing some errors with Bio::DB::Fasta indices. Working with  
different assemblies of a genome, I've been creating symlinks latest/ to  
the latest assembly directory, and genome.fasta to the latest assembly  
fasta file. When I pass latest/genome.fasta to Bio::DB::Fasta, I get a  
genome.fasta.index file, and retrieval works in my script. But then when I  
run a different analysis on it,  or access the same file after a while, I  
get undef for sequences I know for sure to be in the database. Reindexing  
will fix the problem. I'm not certain if this is simply due to the  
symlinks, or a more general issue with Bio::DB::Fasta. Does anyone have  
suggestions?

Venky


-- 
___
Venky Nandagopal
Graduate Student
Eisen Lab
UC Berkeley