gts-rotate - shift the coordinates of a circular sequence
gts-rotate [--version] [-h | --help] [args] amount seqin
gts-rotate takes a single sequence input and shifts the sequence so that
the position matching the location specified by the given locator comes to
the start of the sequence file. If the sequence input is ommited, standard
input will be read instead.
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.
The topology of a sequence that is rotated will be changed to circular.
<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.
-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.
Rotate a sequence 100 bases:
$ gts rotate 100 <seqin>
Rotate a sequence to the first CDS in the sequence:
$ gts rotate CDS <seqin>
gts-rotate currently has no known bugs.
gts-rotate is written and maintained by Kotone Itaya.
gts(1), gts-locator(7), gts-modifier(7), gts-selector(7), gts-seqin(7), gts-seqout(7)