load2sqlitedb1
Load genome sequences and extrinsic evidence hints into a sqlite database
Usage
load2sqlitedb [OPTIONS]
--species=SPECIES
--dbaccess=database.db
inputfilename
Overview
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.
Examples
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
Releases
3 releases since Debian 11 (Bullseye); the text changed 2 times.