getSeq1
Print genome sequences from databases on the standard output
Usage
MySQL:
SQLite:
Overview
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.
Examples
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
Releases
3 releases since Debian 11 (Bullseye); the text changed 2 times.