CSC

Search Sequence Names

This command allows searching for sequences matching a given pattern. The function produces both a list in the text output window and a gap4 "list" of reading names. The highlighted output is clickable, with the left mouse button invoking the contig editor and the right mouse button displaying a popup-menu allowing additional operations (contig editor, template display, reading notes and contig notes).

The text search may be performed as either case-sensitive or case-insensitive. Additionally the pattern search types are available.

sub-string

Matches any reading name where the pattern matches all or part of the name.

wild-cards

Searches for a pattern using normal filename wild-card matching syntax. So * matches any sequence of characters, ? matches any single character, [chars] matches a set of characters defined by chars, and \char matches the literal character char. Character sets may use a minus sign to match a range. For example x*.[fr][1-9] matches any name starting with x and ending with fullstop followed by either f or r followed by a single digit between 1 and 9 inclusive. To match a substring using wild-cards prepend or append the search string with *.

regular expression

This uses the Tcl regular expression syntax to perform a match. These patterns are naturally sub-strings unless anchored to one or both ends using the ^expression$ syntax. A full description of regular expressions is beyond the scope of this manual.