NAME

       load2db - load genome sequences and extrinsic evidence hints into a MySQL database

SYNOPSIS

       load2db [OPTIONS] --species=SPECIES --dbaccess=dbname,host,user,passwd inputfilename

DESCRIPTION

       load2db is a tool to load genome sequences and extrinsic evidence hints into a MySQL database.
       This database must be created before calling load2db.
       When storing genomes/hints of multiple organisms call this program repeatedly for each one.

OPTIONS

       inputfilename refers to a genome file in FASTA format or a hints file in GFF format.

   Mandatory options
       -s, --species=SPECIES
           SPECIES is a name for your species and the same identifier as is used in the treefile and alnfile
           parameters to augustus.

       -d, --dbaccess=dbname,host,user,passwd
           dbname,host,user,passwd are the name of the SQL database, the host name or IP, the database user and
           password

   Additional options
       -c, --chunksize=size (⇐ 1000000)
           This option is only relevant when loading a sequence file.
           The sequences in the input genome are split into chunks of this size so that subsequent retrievals of
           small sequence ranges do not require to read the complete - potentially much longer - chromosome.
           Default Value: 50000

       -h, --help
           Produce help message.

EXAMPLE

             create database before calling load2db:
              $ mysql -u root -p
              > CREATE DATABASE vertebrates;
              > CREATE USER 'myuser'@'%' IDENTIFIED BY 'mypasswd'; /* or whatever the password code is*/
              > GRANT ALL ON vertebrates.* TO 'myuser'@'%' IDENTIFIED BY 'mypasswd';

             load2db --species=mouse --dbaccess=vertebrates,localhost,myuser,mypasswd mouse.fa
             load2db --species=mouse --dbaccess=vertebrates,localhost,myuser,mypasswd mouse.hints.gff
             load2db --species=human --dbaccess=vertebrates,localhost,myuser,mypasswd human.fa
             load2db --species=human --dbaccess=vertebrates,localhost,myuser,mypasswd human.hints.gff

AUTHORS

       AUGUSTUS was written by M. Stanke, O. Keller, S. König, L. Gerischer and L. Romoth.

                                                                                                      LOAD2DB(1)