gt-chseqids1
Change sequence ids by the mapping given in a mapping file.
Usage
gt chseqids
[option ...]
mapping_file
[GFF3_file]
Overview
-
-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”.
Releases
6 releases since Debian 8 (Jessie); the text changed 5 times.