'\" t
.\"     Title: getseq
.\"    Author: [see the "AUTHOR(S)" section]
.\" Generator: Asciidoctor 2.0.20
.\"      Date: 
.\"    Manual: \ \&
.\"    Source: \ \&
.\"  Language: English
.\"
.TH "GETSEQ" "1" "" "\ \&" "\ \&"
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.SH "NAME"
getSeq \- print genome sequences from databases on the standard output
.SH "SYNOPSIS"
.sp
MySQL:
.RS 4
\fBgetSeq\fP [OPTIONS] \-\-species=\fISPECIES\fP \-\-seq=\fISEQUENCE\fP \-\-dbaccess=\fIdbname,host,user,passwd\fP
.RE
.sp
SQLite:
.RS 4
\fBgetSeq\fP [OPTIONS] \-\-species=\fISPECIES\fP \-\-seq=\fISEQUENCE\fP \-\-dbaccess=\fIdbname.db\fP \-\-speciesfilenames=\fISPECIESFILENAMES\fP
.RE
.SH "DESCRIPTION"
.sp
Retrieve a genome sequence from a MySQL and SQLite database or a part of it.
Optionally the reverse complement is printed. Print to standard output.
.SH "OPTIONS"
.SS "Mandatory options"
.sp
\fB\-s\fP, \fB\-\-species\fP=\fISPECIES\fP
.RS 4
SPECIES is the species identifier used when loading the sequence into the database.
.RE
.sp
\fB\-q\fP, \fB\-\-seq\fP=\fISEQUENCE\fP
.RS 4
SEQUENCE is the ID of the sequence to retrieve.
.RE
.sp
\fB\-c\fP, \fB\-\-dbaccess\fP=\fIdatabase\fP
.RS 4
.sp
MySQL:
.RS 4
a string containing dbname, host, user, passwd joined with a comma
.sp
dbname
.RS 4
the name of the SQL database
.RE
.sp
host
.RS 4
the host name or IP
.RE
.sp
user
.RS 4
the database user
.RE
.sp
passwd
.RS 4
users and password
.RE
.RE
.sp
SQLite:
.RS 4
the file name of the SQLite database (must contain a dot)
.RE
.RE
.sp
\fB\-f\fP, \fB\-\-speciesfilenames=SPECIESFILENAMES\fP
.RS 4
This parameter is only recognized for SQLite databases.
.br
SPECIESFILENAMES is the file where the species identifier and the related file names of the sequences are stored.
.br
Format:
.RE
.sp
.if n .RS 4
.nf
.fam C
    Homo sapiens <TAB> /dir/to/genome/human.fa
    Mus musculus <TAB> /dir/to/genome/mouse.fa
.fam
.fi
.if n .RE
.SS "Additional options"
.sp
\fB\-a\fP, \fB\-\-start\fP=\fInumber\fP
.RS 4
Retrieve subsequence starting at this position (coordinates are 1\-based).
.RE
.sp
\fB\-b\fP, \fB\-\-end\fP=\fInumber\fP
.RS 4
Retrieve subsequence ending at this position(coordinates are 1\-based).
.RE
.sp
\fB\-r\fP, \fB\-\-rc\fP
.RS 4
Output the reverse complement of the sequence.
.RE
.sp
\fB\-h\fP, \fB\-\-help\fP
.RS 4
Produce help message.
.RE
.SH "EXAMPLE"
.sp
.if n .RS 4
.nf
.fam C
  MySQL:
    getSeq \-\-species=mouse \-\-seq=chr16 \-\-dbaccess=vertebrates,localhost,myuser,mypasswd
    getSeq \-\-species=human \-\-seq=chr21 \-\-start=32026 \-\-end=32085 \-\-rc \-\-dbaccess=vertebrates,localhost,myuser,mypasswd

  SQLite:
    getSeq \-\-species=mouse \-\-seq=chr16 \-\-dbaccess=vertebrates.db \-\-speciesfilenames=speciesfilenames.tsv
.fam
.fi
.if n .RE
.SH "AUTHORS"
.sp
AUGUSTUS was written by M. Stanke, O. Keller, S. König, L. Gerischer and L. Romoth.