SETKEYS

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Table of Contents
FUNCTION
DESCRIPTION
EXAMPLE
OUTPUT
RELATED PROGRAMS
RESTRICTIONS
SUGGESTIONS
COMMAND-LINE SUMMARY
LOCAL DATA FILES
PARAMETER REFERENCE

FUNCTION

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SetKeys writes a file in your current directory that redefines your keyboard's keys for easier sequence entry with the SeqEd, LineUp, GelEnter and GelAssemble programs and the SeqLab sequence editor. The output file, called set.keys, can be edited if you want to redefine keys that were not considered by the SetKeys program.

DESCRIPTION

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The characters G, A, T, and C are case-shifted keys in three different rows under the left hand. It is difficult to think of a less favorable arrangement for keys that have to be typed quickly and repeatedly. SetKeys addresses this problem by letting you redefine keys to ease nucleic acid sequence entry with SeqEd, LineUp, GelEnter, GelAssemble and the SeqLab sequence editor. SetKeys creates a file named set.keys. It lists nucleotide and ambiguity characters and the keys you wish to use to define them.

Select a key in response to the program prompt for the nucleotides you wish to redefine. If you don't want to redefine a symbol, just answer with <Return>. You can define several keys to have the same meaning.

EXAMPLE

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Here is a sample session with SetKeys:


% setkeys

  Choose key(s) for each nucleotide:

  What key(s) should mean G ?  j
  What key(s) should mean A ?  k
  What key(s) should mean T ?  l
  What key(s) should mean C ?  ;

  Now choose key(s) for the common ambiguity codes:

  What key(s) should mean R ?  u
  What key(s) should mean Y ?  i
  What key(s) should mean N ?  o
  What key(s) should mean <Delete> ?  p

  SetKeys complete: output file is "set.keys"

%

OUTPUT

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Here is the file set.keys that would be written into your current directory from the session above:


 SETKEYS output file for initializing SEQED, LINEUP, GELENTER, GELASSEMBLE,
 and the SEQLAB editor

                        September 11, 1996 09:20          ..
Change j   into   G
Change k   into   A
Change l   into   T
Change ;   into   C
Change u   into   R
Change i   into   Y
Change o   into   N
Change p   into ~^?

RELATED PROGRAMS

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SeqEd, LineUp, GelEnter, GelAssemble, and the SeqLab sequence editor read a file named set.keys if present in your current directory. You can modify this file with a text editor to redefine any GCG accepted sequence character to another character or SeqEd or LineUp control key. EchoKey is an undocumented tool that shows you each terminal key's decimal value and printing character representation. Use the printing character representation from EchoKey to define the key. Use "~^?" to represent the <Delete> key.

RESTRICTIONS

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If you have a file named set.keys in your current directory, then SeqEd, LineUp, GelEnter, and GelAssemble only respond to the keys that you have defined in it; all other keys will be silent. In the SeqLab sequence editor, keys that are not defined in the set.keys file retain their normal definition.

SeqEd, LineUp, GelEnter, and GelAssemble only recognize the GCG sequence character set (see Appendix III). You can also relocate the <Delete> key if you wish.

SUGGESTIONS

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Use a text editor to modify set.keys to your own needs.

COMMAND-LINE SUMMARY

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Complete command-line control is not available for this program.

LOCAL DATA FILES

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None.

PARAMETER REFERENCE

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None.

Printed: December 9, 1998 16:30 (1162)

[ Program Manual | User's Guide | Data Files | Databases ]


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