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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 https://github.com/genometools/genometools/issues.07/29/2020 | GenomeTools 1.6.1 |