---
name: "getSeq"
section: "1"
platform: "linux"
package: "augustus"
version: "3.5.0+dfsg-5"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/getSeq"
---

# getSeq(1)

print genome sequences from databases on the standard output

## NAME

getSeq - print genome sequences from databases on the standard output

## SYNOPSIS

MySQL:

**getSeq** \[OPTIONS\] --species=*SPECIES* --seq=*SEQUENCE* --dbaccess=*dbname,host,user,passwd*

SQLite:

**getSeq** \[OPTIONS\] --species=*SPECIES* --seq=*SEQUENCE* --dbaccess=*dbname.db* --speciesfilenames=*SPECIESFILENAMES*

## DESCRIPTION

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.

## OPTIONS

### Mandatory options

- **-s**, **--species**=*SPECIES*

  SPECIES is the species identifier used when loading the sequence into the database.

- **-q**, **--seq**=*SEQUENCE*

  SEQUENCE is the ID of the sequence to retrieve.

- **-c**, **--dbaccess**=*database*

  MySQL:

  a string containing dbname, host, user, passwd joined with a comma

  dbname

  the name of the SQL database

  host

  the host name or IP

  user

  the database user

  passwd

  users and password

  SQLite:

  the file name of the SQLite database (must contain a dot)

- **-f**, **--speciesfilenames=SPECIESFILENAMES**

  This parameter is only recognized for SQLite databases.\
   SPECIESFILENAMES is the file where the species identifier and the related file names of the sequences are stored.\
   Format:

```
    Homo sapiens <TAB> /dir/to/genome/human.fa
    Mus musculus <TAB> /dir/to/genome/mouse.fa
```

### Additional options

- **-a**, **--start**=*number*

  Retrieve subsequence starting at this position (coordinates are 1-based).

- **-b**, **--end**=*number*

  Retrieve subsequence ending at this position(coordinates are 1-based).

- **-r**, **--rc**

  Output the reverse complement of the sequence.

- **-h**, **--help**

  Produce help message.

## EXAMPLE

```
  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
```

## AUTHORS

AUGUSTUS was written by M. Stanke, O. Keller, S. König, L. Gerischer and L. Romoth.