1. gts-query(1)
3. gts-query(1)

NAME

gts-query - query information from the given sequence

SYNOPSIS

gts-query [--version] [-h | --help] [args] seqin

DESCRIPTION

gts-query takes a single sequence input and reports various information about its features. If the sequence input is ommited, standard input will be read instead. By default, it will output the sequence ID (or a unique sequence number if there are no IDs available), a feature key, its location, and any qualifiers that are common to all of the features present. A single line represents a single feature entry.

This command is best utilized in combination with the gts-select(1) command. Use gts-select(1) to narrow down the features to be extracted, and then apply gts-extract to retrieve information. See the EXAMPLES section for more insight. For a brief summary of a sequence, consider using gts-summary(1).

OPTIONS

<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.

-d <delimiter>, --delimiter=<delimiter>

String to insert between columns. The default delimiter is a tab \t character.

--empty

Allow missing qualifiers to be reported. Unlink GFFs, these columns will be completely empty.

-H, --no-header

Do not print the header line.

-I, --no-seqid

Do not report the sequence identifier.

-K, --no-key

Do not report the feature key.

-L, --no-location

Do not report the feature location.

-n <name>, --name=<name>

Qualifier name(s) to select. Multiple values may be set by repeatedly passing this option to the command. If set, only qualifiers that have the given name will be reported.

--no-cache

Do not use or create cache. See gts-cache(7) for details.

-o <output>, --output=<output>

Output table file (specifying - will force standard output).

--source

Include the source feature(s).

-t <separator>, --separator=<separator>

String to insert between qualifier values. The default separator is a comma , character. By default, the qualifier values will be reported in a CSV format. All commas and double quotes will be escaped, and all newline characters will be replaced with a whitespace.

EXAMPLES

Report information of all CDS features:

$ gts select CDS <seqin> | gts query

Report information of a CDS feature with locus_tag of b0001:

$ gts select CDS/locus_tag=b0001 <seqin> | gts query

Report all of the db_xref qualifiers for every gene in the sequence:

$ gts select gene | gts query -n db_xref
$ gts select gene | gts query --name db_xref

BUGS

gts-query currently has no known bugs.

AUTHORS

gts-query is written and maintained by Kotone Itaya.

SEE ALSO

gts(1), gts-select(1), gts-summary(1), gts-seqin(7), gts-seqout(7)

2. October 2020
3. gts-query(1)