oracular (1) load2sqlitedb.1.gz

NAME

       load2sqlitedb - load genome sequences and extrinsic evidence hints into a SQLite database

SYNOPSIS

       load2sqlitedb [OPTIONS] --species=SPECIES --dbaccess=database.db inputfilename

DESCRIPTION

       load2sqlitedb is a tool to load genome sequences and extrinsic evidence hints into a SQLite database.
       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=database.db
           The file name of the SQLite database that will be opened or created if it does not already exist.

   Additional options
       -c, --chunksize=size
           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. (⇐
           1000000). Default Value: 50000

       -i, --noIdx
           Use this flag to suppress the building of indices on the database tables.
           If you are going to load several genomes and/or hint files in a row, this option is recommended to
           speed up the loading. But make sure to build indices with --makeIdx after all genomes/hints are
           loaded. Otherwise, data retrieval operations can be very slow.

       -m, --makeIdx
           Use this flag to build the indices on the database tables after loading several genomes and/or hint
           files with --noIdx.
           Only call this once for all species, e.g. load2sqlitedb --makeIdx --dbaccess=database.db

       -r, --clean
           Makes a clean load deleting existing hints/genome for the species from the database.+ When called
           with a gff file, only the hints for the species are delete, but not the genome.
           When called with a fasta file, both hints and genome for the species are deleted.

       -h, --help
           Produce help message.

EXAMPLE

             load2sqlitedb --species=mouse --dbaccess=vertebrates.db mouse.fa
             load2sqlitedb --species=mouse --dbaccess=vertebrates.db mouse.hints.gff
             load2sqlitedb --species=human --dbaccess=vertebrates.db human.fa
             load2sqlitedb --species=human --dbaccess=vertebrates.db human.hints.gff

AUTHORS

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

                                                                                                LOAD2SQLITEDB(1)