| LOAD2SQLITEDB(1) | LOAD2SQLITEDB(1) |
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
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.
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
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.
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.