gts-delete - delete a region of the given sequence(s)
gts-delete [--version] [-h | --help] [args] locator seqin
gts-delete takes a single sequence input and deletes the specified region.
If the sequence input is ommited, standard input will be read instead. The
region to be deleted is specified using a locator.
A locator consists of a location specifier and a modifier. A location specifier
may be a modifier, a point location, a range location, or a selector.
The syntax for a locator is [specifier][@modifier]. See gts-locator(7) for a
more in-depth explanation of a locator. Refer to the EXAMPLES for some examples
to get started.
Features that were present in the region being deleted will be shifted as being
in between the bases at the deletion point. Such features can be completely
erased from the sequence if the -e or --erase option is provided.
<locator>A locator string ([specifier][@modifier]). See gts-locator(7) for more
details.
<seqin>Input sequence file (may be omitted if standard input is provided). See gts-seqin(7) for a list of currently supported list of sequence formats.
-e, --eraseRemove features contained in the deleted regions.
-F <format>, --format=<format>Output file format (defaults to same as input). See gts-seqout(7) for a list of currently supported list of sequence formats. The format specified with this option will override the file type detection from the output filename.
--no-cacheDo not use or create cache. See gts-cache(7) for details.
-o <output>, --output=<output>Output sequence file (specifying - will force standard output). The
output file format will be automatically detected from the filename if none
is specified with the -F or --format option.
Delete bases 100 to 200:
$ gts delete 100..200 <seqin>
Delete all regions of misc_feature and its features:
$ gts delete --erase misc_feature <seqin>
Delete 20 bases upstream of every CDS:
$ gts delete CDS^-20..^ <seqin>
gts-delete currently has no known bugs.
gts-delete is written and maintained by Kotone Itaya.
gts(1), gts-insert(1), gts-locator(7), gts-modifier(7), gts-selector(7), gts-seqin(7), gts-seqout(7)