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