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.\"     Title: load2db
.\"    Author: [see the "AUTHOR(S)" section]
.\" Generator: Asciidoctor 2.0.20
.\"      Date: 
.\"    Manual: \ \&
.\"    Source: \ \&
.\"  Language: English
.\"
.TH "LOAD2DB" "1" "" "\ \&" "\ \&"
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.SH "NAME"
load2db \- load genome sequences and extrinsic evidence hints into a MySQL database
.SH "SYNOPSIS"
.sp
\fBload2db\fP [OPTIONS] \-\-species=\fISPECIES\fP \-\-dbaccess=\fIdbname,host,user,passwd\fP \fIinputfilename\fP
.SH "DESCRIPTION"
.sp
\fBload2db\fP is a tool to load genome sequences and extrinsic evidence hints into a MySQL database.
.br
This database must be created before calling \fBload2db\fP.
.br
When storing genomes/hints of multiple organisms call this program repeatedly for each one.
.SH "OPTIONS"
.sp
\fIinputfilename\fP refers to a genome file in FASTA format or a hints file in GFF format.
.SS "Mandatory options"
.sp
\fB\-s\fP, \fB\-\-species\fP=\fISPECIES\fP
.RS 4
SPECIES is a name for your species and the same identifier as is used in the treefile and alnfile parameters to augustus.
.RE
.sp
\fB\-d\fP, \fB\-\-dbaccess\fP=\fIdbname,host,user,passwd\fP
.RS 4
dbname,host,user,passwd are the name of the SQL database, the host name or IP, the database user and password
.RE
.SS "Additional options"
.sp
\fB\-c\fP, \fB\-\-chunksize\fP=\fIsize\fP (\(lA 1000000)
.RS 4
This option is only relevant when loading a sequence file.
.br
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
.RE
.sp
\fB\-h\fP, \fB\-\-help\fP
.RS 4
Produce help message.
.RE
.SH "EXAMPLE"
.sp
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  create database before calling load2db:
   $ mysql \-u root \-p
   > CREATE DATABASE vertebrates;
   > CREATE USER \*(Aqmyuser\*(Aq@\*(Aq%\*(Aq IDENTIFIED BY \*(Aqmypasswd\*(Aq; /* or whatever the password code is*/
   > GRANT ALL ON vertebrates.* TO \*(Aqmyuser\*(Aq@\*(Aq%\*(Aq IDENTIFIED BY \*(Aqmypasswd\*(Aq;

  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
.fam
.fi
.if n .RE
.SH "AUTHORS"
.sp
AUGUSTUS was written by M. Stanke, O. Keller, S. König, L. Gerischer and L. Romoth.