gts-insert - insert guest sequence(s) into the input sequence(s)
gts-insert [--version] [-h | --help] [args] locator guest host
gts-insert takes two sequence inputs: a guest sequence input and a host
sequence input, and inserts the sequences contained in the guest sequence
input into the sequences contained in the host sequence input. If the host
sequence input is omitted, standard input will be read instead. For each
sequence in the guest sequence input, a copy of each of the host sequence
input will be created. Each guest sequence will then be inserted into the
location(s) specified by the locator in the host sequence.
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 at the point of insertion will be split to form
a joined location. Such features can be instead expanded if the -e or
--embed option is provided. Any features present in the guest sequence
will be transferred to the corresponding locations after being inesrted into
the host sequence.
There is also a similar command in gts(1) designated gts-infix(1). While gts-insert inserts guest sequences into the primary sequence input, gts-infix(1) inserts the primary sequence input into the host sequences. Use gts-insert when you want to insert another sequence into the sequence that ou are working on in a pipeline. Note that all of the guest sequences will be read into memory when using gts-insert, and all of the host sequences will be read into memory when using gts-infix(1). If memory availability may be an issue, make sure to use the command that will read in the smaller file.
<locator>A locator string ([specifier][@modifier]). See gts-locator(7) for more
details.
<guest>Guest sequence file (will be interpreted literally if preceded with @). See gts-seqin(7) for a list of currently supported list of sequence formats.
<host>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, --embedExtend existing feature locations when inserting instead of splitting them.
-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.
Insert a sequence at position 100:
$ gts insert 100 <guest> <host>
Insert a sequence 20 bases upstream of each CDS:
$ gts insert CDS@^-20 <guest> <host>
gts-insert currently has no known bugs.
gts-insert is written and maintained by Kotone Itaya.
gts(1), gts-infix(1), gts-delete(1), gts-locator(7), gts-modifier(7), gts-selector(7), gts-seqin(7), gts-seqout(7)