chseqids = {
chr1 = "seq1",
chr2 = "seq2"
}
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:
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 https://github.com/genometools/genometools/issues.