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load_genbankp - Online in the Cloud

Run load_genbankp in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

This is the command load_genbankp that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

NAME


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

SYNOPSIS


% load_genbank.pl -d genbank -f localfile.gb
% load_genbank.pl -d genbank -a AP003256

NOTE: The script bp_genbank2gff.pl in the BioPerl distribution is the same as this script.

DESCRIPTION


This script loads a Bio::DB::GFF database with the features contained in a either a local
genbank file or an accession that is fetched from genbank. Various command-line options
allow you to control which database to load and whether to allow an existing database to
be overwritten.

This script currently only uses MySQL, though it is a proof-of- principle and could easily
be extended to work with other RDMS that are supported by GFF through adaptors.

COMMAND-LINE OPTIONS


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

--create Force creation and initialization of database
--dsn <dsn> Data source (default dbi:mysql:test)
--user <user> Username for mysql authentication
--pass <password> Password for mysql authentication
--proxy <proxy> Proxy server to use for remote access
--file Arguments that follow are Genbank/EMBL file names (default)
--accession Arguments that follow are genbank accession numbers
--stdout Write converted GFF file to stdout rather than loading

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