gts-pick - pick sequence(s) from multiple sequences
gts-pick [--version] [-h | --help] [args] list seqin
gts-pick takes a single sequence input and returns the sequences specified
by the list option. If the sequence input is ommited, standard input will be
read instead. The list option is equivalent to that of cut(1). Sequence
numbering starts at 1. Specifying the -f or --feature option will output
all sequences but pick the features matching the list option.
<list>List of sequences to pick (identical to the list option in cut). A list is
a comma separated set of numbers and/or number ranges. Number ranges
consist of a number, a dash character -, and a second number. A number
range will select the sequences from the first number to the second,
inclusive. Numbers may be preceded by a dash, which selects all sequences
from 1 up to the number. Numbers may be followed by a dash, which selects
all sequences from the number to the last.
<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, --featurePick features instead of sequences.
-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.
Pick the first sequence in the file:
$ gts pick 1 <seqin>
Pick the first ten features from each sequence in the file:
$ gts pick -f -10 <seqin>
gts-pick currently has no known bugs.
gts-pick is written and maintained by Kotone Itaya.
gts(1), gts-seqin(7), gts-seqout(7) cut(1)