load2db(1) · carta

Usage

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

Overview

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.

Examples

  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

Releases

3 releases since Debian 11 (Bullseye); the text changed 2 times.

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