BP_FAST_LOAD_GFF(1) User Contributed Perl Documentation BP_FAST_LOAD_GFF(1)NAMEbp_fast_load_gff.pl - Fast-load a Bio::DB::GFF database from GFF files.
SYNOPSIS
% bp_fast_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 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.
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 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
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
the load.
--Temporary Location of a writable scratch directory
SEE ALSO
Bio::DB::GFF, bulk_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 v5.20.2 2015-09-15 BP_FAST_LOAD_GFF(1)
