NAME

       gt-chseqids - Change sequence ids by the mapping given in mapping_file.

SYNOPSIS

       gt chseqids [option ...] mapping_file [GFF3_file]

OPTIONS

       -sort
           sort the GFF3 features after changing the sequence ids (memory consumption is proportional to the
           input file size) (default: no)

       -v
           be verbose (default: no)

       -o
           redirect output to specified file (default: undefined)

       -gzip
           write gzip compressed output file (default: no)

       -bzip2
           write bzip2 compressed output file (default: no)

       -force
           force writing to output file (default: no)

       -help
           display help and exit

       -version
           display version information and exit

DESCRIPTION

       File format for mapping_file:

       The supplied mapping file defines a mapping table named “chseqids”. It maps the sequence-regions given in
       the GFF3_file to other names. It can be defined as follows:

       chseqids = { chr1 = "seq1", chr2 = "seq2" }

       When this example is used, all sequence ids “chr1” will be changed to “seq1' ' and all sequence ids
       ``chr2” to “seq2”.

AUTHOR

       Report bugs to <gt-users@genometools.org>.

                                                   10/07/2012                                     GT-CHSEQIDS(1)