Tcl Scripting of Gap4

• Introduction
• Low-level IO Access
• Utility Commands
• Main Commands
• The Editor Widget
• The EdNames Widget

Introduction

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

• Introduction
• IO Primitives
• Gap-level IO Commands

Introduction

FIXME: Add intro here