1. gts-select(1)
3. gts-select(1)

NAME

gts-select - select features using the given feature selector(s)

SYNOPSIS

gts-select [--version] [-h | --help] [args] selector seqin

DESCRIPTION

gts-select takes a selector and a single sequence input, and selects the features which satisfy the selector criteria. If the sequence input is ommited, standard input will be read instead. A selector takes the form [feature_key][/[qualifier1][=regexp1]][/[qualifier2][=regexp2]].... See gts-selector(7) for more details.

gts-select serves as a central command, allowing the user to filter out features for use in other commands like gts-extract(1) and gts-query(1). See the EXAMPLES section for more insight.

OPTIONS

<selector>

Feature selector (syntax: [feature_key][/[qualifier1][=regexp1]][/[qualifier2][=regexp2]]...). See gts-selector(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-cache

Do 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.

-s <strand>, --strand=<strand>

Strand to select features from (both, forward, or reverse). If forward is specified, only features that reside strictly on the forward strand (features with non-complement locations or join/order locations whose locations are all non-complement). The inverse is true for reverse.

-v, --invert-match

Select features that do not match the given criteria.

EXAMPLES

Select all of the CDS features:

$ gts select CDS <seqin>

Select all features with locus_tag of b0001:

$ gts select /locus_tag=b0001 <seqin>

Select all features with the qualifier translation:

$ gts select /translation <seqin>

Select all features with a qualifier value matching recombinase

$ gts select /=recombinase <seqin>

BUGS

gts-select currently has no known bugs.

AUTHORS

gts-select is written and maintained by Kotone Itaya.

SEE ALSO

gts(1), gts-query(1), gts-selector(7), gts-seqin(7), gts-seqout(7)

2. May 2021
3. gts-select(1)