Man page - getseq(1)

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Manual

GETSEQ

NAME
SYNOPSIS
DESCRIPTION
OPTIONS
Mandatory options
Additional options
EXAMPLE
AUTHORS

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.