BP_BULK_LOAD_GFF(1p)					User Contributed Perl Documentation				      BP_BULK_LOAD_GFF(1p)

NAME

       bulk_load_gff.pl - Bulk-load a Bio::DB::GFF database from GFF files.

SYNOPSIS

	 % 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.

       Local data may now be uploaded to a remote server via the --local option with the database host specified in the dsn, e.g.
       dbi:mysql:test:db_host

       The adaptor used is dbi::mysqlopt.  There is currently no way to change this.

       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.

       Note that Windows users must use the --create option.

       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.

COMMAND-LINE OPTIONS
       Command-line options can be abbreviated to single-letter options.  e.g. -d instead of --database.

	  --database <dsn>	Database name (default dbi:mysql:test)
	  --adaptor		Adaptor name (default mysql)
	  --create		Reinitialize/create data tables without asking
	  --user		Username to log in as
	  --fasta		File or directory containing fasta files to load
	  --long_list		Directory containing a very large number of
				GFF and/or FASTA files
	  --password		Password to use for authentication
				  (Does not work with Postgres, password must be
				  supplied interactively or be left empty for
				  ident authentication)
	  --maxbin		Set the value of the maximum bin size
	  --local		Flag to indicate that the data source is local
	  --maxfeature		Set the value of the maximum feature size (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

SEE 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.

perl v5.14.2							    2012-03-02						      BP_BULK_LOAD_GFF(1p)