1. gts-locator(7)
  2. gts-locator(7)

NAME

gts-locator

gts-locator(7) -- patterns to refer to locations in a sequence

SYNOPSIS

[selector|point|range][@modifier]

DESCRIPTION

gts-locators are patterns for specifying locations within a sequence. A locator consists of a location specifier and a modifier. A location specifier is one of a modifier, a selector, a point location, or range location. A selector takes the form [feature_key][/[qualifier1][=regexp1]][/[qualifier2][=regexp2]].... See gts-selector(7) for more details. A point location is simply a single integer that directly specifies a single point in the sequence (starting at 1). A range location is a pair of integers connected with .. (starting at 1), which is identical to the notation of a feature range location. However, the range location of a locator may specify a modifier, in which case the ^ represents the beginning of the sequence and the $ represents the end of the sequence. The locations specified by the location specifier can be modified using a modifier. A modifier can take one of five forms: ^[(+|-)n], $[[(+|-)m]], ^[(+|-)n]..$[(+|-)m], ^[(+|-)n]..^[(+|-)m], or $[(+|-)n]..$[(+|-)m]. See gts-modifier(7) for more details.

EXAMPLES

Locate the sequence 100 bases upstream of a CDS:

CDS@^-100..^

Extend a location 20 bases upstream and downstream of a gene:

gene@^-20..$+20

Locate a range between 100 and 200 bases:

100..200

SEE ALSO

gts(1), gts-delete(1), gts-infix(1) gts-insert(1), gts-rotate(1), gts-split(1), gts-modifier(7), gts-selector(7)

  1. October 2020
  2. gts-locator(7)