GT-CHSEQIDS(1)

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>.