GETSEQ(1) | GETSEQ(1) |
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:
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.