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


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


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.


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.


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


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