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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 overwritten.

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 --local option.

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 10.

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 <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
the load.
--Temporary Location of a writable scratch directory

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