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.

                                                                                                       GETSEQ(1)