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GT-CHSEQIDS(1) GenomeTools Manual GT-CHSEQIDS(1)

NAME

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

SYNOPSIS

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

DESCRIPTION

-sort [yes|no]
sort the GFF3 features after changing the sequence ids (memory consumption is proportional to the input file size) (default: no)
-v [yes|no]
be verbose (default: no)
-o [filename]
redirect output to specified file (default: undefined)
-gzip [yes|no]
write gzip compressed output file (default: no)
-bzip2 [yes|no]
write bzip2 compressed output file (default: no)
-force [yes|no]
force writing to output file (default: no)
-help
display help and exit
-version
display version information and exit
File format for mapping_file:
The supplied mapping file defines a mapping table named “chseqids”. It maps the sequence-region entries 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”.

REPORTING BUGS

Report bugs to <gt-users@genometools.org>.
07/29/2016 GenomeTools 1.5.9