Command and Keystroke Differences Between OpenVMS and UNIX

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Table of Contents

Overview

Command-Line Differences

OpenVMS

UNIX

Control-Key Differences

Program Differences

Wisconsin Package Program Supported Only on OpenVMS VAX

Wisconsin Package Programs Supported Only on UNIX

Program Names Modified From Previous Wisconsin Package Versions

UNIX Metacharacter Descriptions

Summary of OpenVMS/UNIX Command-Line Differences


Overview

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This appendix is intended for users whose sites have switched from the OpenVMS version of the Wisconsin Package to the UNIX version (or vice versa). You will find the following information in this appendix:

Command-Line Differences

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OpenVMS

Command-Line Syntax: $ Command /PARameter

UNIX

Command-Line Syntax: % command -PARameter

Control-Key Differences

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The following table lists the control key combinations that are different between UNIX and OpenVMS.

OpenVMS UNIX Description
<Ctrl>C
<Ctrl>Y
<Ctrl>c Ends a program.
Not Available <Ctrl>z Suspends a program.
<Ctrl>Z <Ctrl>d End of file.

Program Differences

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Wisconsin Package Program Supported Only on OpenVMS VAX

PlotMetaFile Plots a GKS metafile on any GKS supported device. (GKS is not supported on UNIX or OpenVMS AXP.)

Wisconsin Package Programs Supported Only on UNIX

Name Displays and manipulates the Wisconsin Package logical names. For more information, see the Program Manual.
Symbol Displays and manipulates the Wisconsin Package symbols. For more information, see the Program Manual.

(Logical names and symbols are an innate part of the OpenVMS operating system. However, GCG created the logical name and symbol service on UNIX.)

Program Names Modified From Previous Wisconsin Package Versions

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Because of conflicts between Wisconsin Package program names and UNIX operating system commands, some Wisconsin Package program names have been modified. The name changes have occurred since Version 7. The following program names are correct for both OpenVMS and UNIX in Version 10:

Previous Versions' Program Names Current
Program Names
Clear ClearPlot
Echo EchoKey
Extract ExtractPeptide
Find FindPatterns
Shift ShiftOver
Strings StringSearch
ToBLAST GCGToBLAST
NewDiverge Diverge

UNIX Metacharacter Descriptions

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The UNIX shell recognizes some characters as having special meaning (see % man csh for more information). Although these characters, called shell metacharacters, may have no particular meaning in a OpenVMS environment, they do have meaning in a UNIX environment.

The following table lists common UNIX shell metacharacters and their descriptions.

Character Example Description
$
(dollar sign)
% cd $GCGCOREROOT Specifies that the non-blank characters following the $ are the name of a shell or environment variable.
&
(ampersand)
% fasta in:drogpdh -def & Specifies that the part of the command line preceding the & should be run in the background.
>
(greater than)
% fasta in:drogpdh -def > fasta.log & Specifies that the output from the part of the command line preceding the > should be redirected into a file with the name of the word following it.
<
(less than)
% cat < fasta.log Specifies that the command input be taken from a file following the <.
|
(pipe)
% typedata in:drogpdh | more Specifies that the output from the command should be piped into the command following the |.
!
(exclamation point)
% !!
% !21
Specifies a history substitution, that is, use of a previously entered command line. % !! recalls your previous command. % !n recalls command n on your list of previously entered commands.
\
(backslash)
% stringsearch gb_pr:* drb3\$ -Default Specifies that the character following the \ should be prevented from shell interpretation.
( )
(parentheses)
% (cd adhdir ; fetch in:droadh*) Specifies that the command line enclosed in ( ) should be executed in a subshell.
;
(semicolon)
% cd adhdir ; fetch in:droadh* Specifies that the command line is two commands (one on both sides of the semicolon).
`
(backquote)
% cd `name -f GenDocData` Specifies that the text enclosed between a pair of backquotes should be run as a command first, before submitting its output to the rest of the command line.
'
(single quotation marks)
% stringsearch gb_pr:* 'drd3$' -Default Specifies that the shell should not interpret the characters enclosed within the single quotation marks. You can include spaces, * or ? wildcards, or the $ within the single quotes.
"
(double quotation marks)
% stringsearch in:* "light chain" -Default Specifies that the shell should not interpret the characters enclosed in double quotes, including spaces and * or ? wildcards. Note that the $ shell variable will be interpreted.
*
(asterisk)
% ls gam* Used as a wildcard in a filename specification, it specifies zero or more of any character.
?
(question mark)
% fetch ?gamma.seq Used as a wildcard in a filename specification, specifies one of any character.
~
(tilde)
% more ~/fasta.log Used as a wildcard in a filename specification, expands to the home directory of the user.

Note: Because the asterisk (*) and question mark (?) are frequently used characters for specifying ambiguous database entries, GCG provides an alias for each Wisconsin Package command to disable globbing. Therefore, you can freely use these characters on the command line when invoking Wisconsin Package programs.


Summary of OpenVMS/UNIX Command-Line Differences

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The following table compares the general rules for entering Wisconsin Package command-line information in OpenVMS and UNIX.

Topic OpenVMS UNIX
Abbreviations You can abbreviate most commands. The documentation indicates the abbreviation in bold. You cannot abbreviate commands.
You can abbreviate most parameters. The documentation indicates the abbreviation in bold uppercase. Same as OpenVMS.
Case Sensitivity Commands are case insensitive. Commands are always lowercase.
Parameter qualifiers are case insensitive. Same as OpenVMS.
Parameter values are case insensitive. The case sensitivity for parameter values varies depending on the parameter. For example, if you provide a filename as a parameter value, it is case sensitive.
Directory names are case insensitive. Directory names are case sensitive.
File names are case insensitive. File names are case sensitive.
Database names, logical names, and sequence entries are case insensitive. Same as OpenVMS.
Naming Devices The syntax for device names vary from that of directory or file names. For example

LTA13: (printer)
DISK:[Dir]FileName.Txt (file)
The syntax for device names is the same as for directory and filenames. For example

/dev/tty16 (printer)
/usr/dir/filename.txt (file)
You can name and refer to disks (DISK:). You cannot name or refer to disks.
Parameters A slash (/) indicates a command-line parameter. An equal sign (=) indicates a parameter that requires a value. Not all parameters require values. For example

/OUT=MyFile.Test /Default
A dash (-) indicates a command-line parameter. An equal sign (=) indicates a parameter that requires a value. Not all parameters require a value. For example

-OUT=myfile.test -Default
Spaces Spaces are ignored between a command and its parameter(s). Spaces are required (at least one) between a command and its parameters.
Spaces are ignored between command-line parameters. Spaces are required (at least one) between command-line parameters.
Spaces are not allowed between a parameter and its value. Same as OpenVMS.
Wildcards The asterisk (*) wildcard serves as an ambiguous replacement for a character or group of characters; the * means "anything or nothing."

For example gamma.* matches all files that begin with "gamma." gam*.map matches all files that begin with "gam" and have an extension of "map."
Same as OpenVMS.
The percent sign (%) wildcard serves as an ambiguous replacement for one character. You can use multiple % to specify a defined number of ambiguous characters.

For example gamma.s%% matches all files that begin with "gamma" and have a three-letter extension starting with "s."
The question mark (?) wildcard serves as an ambiguous replacement for one character. You can use multiple ? to specify a defined number of ambiguous characters.

For example gamma.s?? matches all files that begin with "gamma" and have a three-letter extension starting with "s."

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