This script loads a Bio::DB::GFF database with the features contained
in a list of GFF files and/or FASTA sequence files. You must use the
exact variant of GFF described in Bio::DB::GFF. Various
command-line options allow you to control which database to load and
whether to allow an existing database to be overwritten.
This script uses the Bio::DB::GFF interface, and so works with all
database adaptors currently supported by that module (MySQL, Oracle,
PostgreSQL soon). However, it is slow. For faster loading, see the
MySQL-specific bp_bulk_load_gff.pl and bp_fast_load_gff.pl scripts.
If the filename is given as - then the input is taken from standard
input. Compressed files (.gz, .Z, .bz2) are automatically
FASTA format files are distinguished from GFF files by their filename
extensions. Files ending in .fa, .fasta, .fast, .seq, .dna and their
uppercase variants are treated as FASTA files. Everything else is
treated as a GFF file. If you wish to load -fasta files from STDIN,
then use the -f command-line swith with an argument of -, as in
gunzip my_data.fa.gz | bp_fast_load_gff.pl -d test -f -
On the first load of a database, you will see a number of unknown
table errors. This is normal.
About maxfeature: the default value is 100,000,000 bases. If you have
features that are close to or greater that 100Mb in length, then the
value of maxfeature should be increased to 1,000,000,000, or another
power of 10.