gts-extract - extract the sequences referenced by the features
gts-extract [--version] [-h | --help] [args] seqin
gts-extract takes a single sequence input and return the sequences
associated with each feature. If the sequence input is ommited, standard input
will be read instead. Additionally, if the locator argument is given, the
regions associated with the locators will be extracted.
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.
This command is best utilized in combination with the gts-select(1) command. Use gts-select(1) to narrow down the sequence regions to be extracted, and then apply gts-extract to retrieve the sequences. See the EXAMPLES section for more insight.
<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.
Retrieve the sequences of all CDS features:
$ gts select CDS <seqin> | gts extract
Retrieve the sequence 100 bases upstream of all CDS features:
$ gts select CDS <seqin> | gts extract -m ^-100..^
$ gts select CDS <seqin> | gts extract --range ^-100..^
Retrieve the sequence 100 bases downstream of all CDS features:
$ gts select CDS <seqin> | gts extract -m $..$+100
$ gts select CDS <seqin> | gts extract --range $..$+100
gts-extract currently has no known bugs.
gts-extract is written and maintained by Kotone Itaya.
gts(1), gts-select(1), gts-modifier(7), gts-seqin(7), gts-seqout(7)