DOKK / manpages / debian 11 / augustus / getSeq.1.en
GETSEQ(1)   GETSEQ(1)

getSeq - print genome sequences from databases on the standard output

MySQL:

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

SQLite:

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

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.

-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

-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.



  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

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