gts-search(1) - search for a subsequence and annotate its results

gts-search(1)
gts-search(1)

NAME

gts-search - search for a subsequence and annotate its results

SYNOPSIS

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

DESCRIPTION

gts-search takes a query and a single input sequence, and marks the regions where the query sequences were found. If the sequence input is ommited, standard input will be read instead. If a file with a filename equivalent to the query value exists, it will be opened and read by the command. If it does not, the command will interpret the query string as a sequence. The query sequence(s) will be treated as an oligomer. In order to find perfect matches only, use the -e or --exact option. By default, regions are marked as misc_features without any qualifiers. Use the -k or --key option and -q or --qualifier option so you can easily discover these features later on with gts-select(1). See the EXAMPLES section for more insight.

OPTIONS

<query>: Query sequence file (will be interpreted literally if preceded with @). See gts-seqin(7) for a list of currently supported list of sequence formats.
<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.
-e, --exact: Match the exact pattern even for ambiguous letters.
-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.
-k <key>, --key=<key>: Key for the reported oligomer region features. The default feature key is misc_feature.
--no-cache: Do not use or create cache. See gts-cache(7) for details.
--no-complement: Do not match the complement strand.
-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.
-q <qualifier>, --qualifier=<qualifier>: Qualifier key-value pairs (syntax: key=value)). Multiple values may be set by repeatedly passing this option to the command.

EXAMPLES

Search for query and retrieve the regions 100 bases around the matches.

$ gts search -q note=search <query> <seqin> | \
  gts select misc_feature/note=search | \
  gts extract -m '^-100..$+100'

BUGS

gts-search currently has no known bugs.

AUTHORS

gts-search is written and maintained by Kotone Itaya.