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bp_load_gff.pl - Load a Bio::DB::GFF database from GFF files.


% bp_load_gff.pl -d testdb -u user -p pw
--dsn 'dbi:mysql:database=dmel_r5_1;host=myhost;port=myport'
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 uses the Bio::DB::GFF interface, and so works with all database adaptors
currently supported by that module (MySQL, Oracle, PostgreSQL soon). However, it is slow.
For faster loading, see the MySQL-specific bp_bulk_load_gff.pl and bp_fast_load_gff.pl

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 -

On the first load of a database, you will see a number of "unknown table" errors. This is

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, or another power of 10.


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

--dsn <dsn> Data source (default dbi:mysql:test)
--adaptor <adaptor> Schema adaptor (default dbi::mysqlopt)
--user <user> Username for mysql authentication
--pass <password> Password for mysql authentication
--fasta <path> Fasta file or directory containing fasta files for the DNA
--create Force creation and initialization of database
--maxfeature Set the value of the maximum feature size (default 100 Mb; 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.
--upgrade Upgrade existing database to current schema
--gff3_munge Activate GFF3 name munging (see Bio::DB::GFF)
--quiet No progress reports
--summary Generate summary statistics for drawing coverage histograms.
This can be run on a previously loaded database or during
the load.

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