bp_fast_load_gff.pl - Fast-load a Bio::DB::GFF database from GFF files.
% bp_fast_load_gff.pl -d testdb dna1.fa dna2.fa features1.gff features2.gff ...
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
This script is similar to load_gff.pl, but is much faster. However, it is
hard-coded to use MySQL and probably only works on Unix platforms due to its
reliance on pipes. See bp_load_gff.pl for an incremental loader that works
with all databases supported by Bio::DB::GFF, and bp_bulk_load_gff.pl for a
fast MySQL loader that supports all platforms.
If the filename is given as "-" then the input is taken from standard
input. Compressed files (.gz, .Z, .bz2) are automatically uncompressed.
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 -
The nature of the load requires that the database be on the local machine and
that the indicated user have the "file" privilege to load the tables
and have enough room in /usr/tmp (or whatever is specified by the \$TMPDIR
environment variable), to hold the tables transiently. If your MySQL is
version 3.22.6 and was compiled using the "load local file" option,
then you may be able to load remote databases with local data using the
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. This value must be a power of
If the list of GFF or fasta files exceeds the kernel limit for the maximum
number of command-line arguments, use the --long_list /path/to/files option.
The adaptor used is dbi::mysqlopt. There is currently no way to change this.
Command-line options can be abbreviated to single-letter options. e.g. -d
instead of --database.
--database <dsn> Mysql database name
--create Reinitialize/create data tables without asking
--local Try to load a remote database using local data.
--user Username to log in as
--fasta File or directory containing fasta files to load
--password Password to use for authentication
--long_list Directory containing a very large number of
GFF and/or FASTA files
--maxfeature Set the value of the maximum feature size (default 100Mb; must be a power of 10)
--group A list of one or more tag names (comma or space separated)
to be used for grouping in the 9th column.
--gff3_munge Activate GFF3 name munging (see Bio::DB::GFF)
--summary Generate summary statistics for drawing coverage histograms.
This can be run on a previously loaded database or during
--Temporary Location of a writable scratch directory
Bio::DB::GFF, bulk_load_gff.pl, load_gff.pl
Lincoln Stein, email@example.com
Copyright (c) 2002 Cold Spring Harbor Laboratory
This library is free software; you can redistribute it and/or modify it under
the same terms as Perl itself. See DISCLAIMER.txt for disclaimers of