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Tcl Scripting of Gap4


This chapter describes the gap4 scripting language. The language is an extension of the Tcl and Tk languages. This manual does not contain information on using Tcl and Tk itself - only our extensions.

For the purpose of consistency, many gap4 commands take identical arguments. To simplify the documentation and to remove redundancy these arguments are only briefly discussed with each command description. However first we need to describe the terminology used throughout this manual.

Reading identifier
Used to specify a reading. It can consist of the reading's unique name, a hash followed by its reading number, or if it is at the start of a contig, an equals followed by the contig number. Eg fred.s1, #12, or =2.
Contig identifier
A contig is identified by any reading within it, so all reading identifiers are contig identifiers. However when a contig identifier is displayed by a command it typically chooses the left most reading name. If a contig number is known, simply use =number as a contig identifier.

Common arguments:

-contigs contig_list
Contig_list is a Tcl list of contig identifiers. If an item in the list is itself a list, then the first element of the list is the identifier and the second and third elements specify a range within that contig. Eg -contigs {read1 {read5 1000 2000} read6}
-readings reading_list
Reading_list is a Tcl list of reading identifiers. Eg -reading_list {read1 read2}
-contig contig_identifier
Specifies a single contig by an indentifier.
-reading reading_identifier
Specifies a single reading by an identifier.
-cnum contig_number
Specifies a contig by its number (NB: this not the same as a reading number within that contig).
-rnum reading_number
Specifies a reading by its number.
-io io_handle
Specifies an IO handle by a numerical value as returned from a previous open_db command.

Low-level IO Access


FIXME: Add intro here

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This page is maintained by staden-package. Last generated on 1 March 2001.