[Bioperl-l] Trouble with Bio::DB::Fasta and large files

Tyler tsw@uclink4.berkeley.edu
Tue, 5 Nov 2002 16:32:29 -0800

I have been using Bio::DB::Fasta to extract sequences from fasta BLAST 
databases for zebrafish and fugu with no problems. I've used both the 
tied hash and object oriented implementations and they work great with 
these databases. Thanks Lincoln.

However, when trying to use Bio::DB::Fasta on local mouse or human 
genome databases (ensembl raw data) they throw the "Invalid file or 
dirname" exception. The mouse fasta file is 2.7GB and the human one is 
3.2GB, as opposed to 1.2GB for zebrafish and 340MB for fugu. All 
scripts are the same except for the name of the database file. All 
databases work fine with standalone blast (both the web interface and 
the bioperl interface).

Is there a work around for dealing with these extremely large files?