NAME
bp_bulk_load_gff.pl - Bulk-load a Bio::DB::GFF database from GFF files.
SYNOPSIS
% bp_bulk_load_gff.pl -d testdb dna1.fa dna2.fa features1.gff features2.gff ...DESCRIPTION
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 differs from bp_load_gff.pl in that it is hard-coded to use MySQL and cannot perform incremental loads. See bp_load_gff.pl for an incremental loader that works with all databases supported by Bio::DB::GFF, and bp_fast_load_gff.pl for a MySQL loader that supports fast incremental loads.
NOTES
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 bulk 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.
The adaptor used is dbi::mysqlopt. There is currently no way to change this.
Note that Windows users must use the --create option.
COMMAND-LINE OPTIONS
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
--user Username to log in as
--fasta File or directory containing fasta files to load
--password Password to use for authenticationSEE ALSO
Bio::DB::GFF, fast_load_gff.pl, load_gff.pl
AUTHOR
Lincoln Stein, lstein@cshl.org
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 warranty.