SPEW

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

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

FUNCTION

[ Top | Next ]

Spew sends a GCG sequence from the computer that runs the Wisconsin Package to a personal computer acting as a terminal.

DESCRIPTION

[ Previous | Top | Next ]

Spew identifies a sequence file that you want to transfer to your microcomputer, then it waits until you type <Ctrl>F before it sends the sequence data from your file to your terminal. Before Spew sends the characters, you must open the receiving file on the microcomputer by means of the microcomputer's communications software. Spew sends the sequence as a stream of characters with no characters other than the sequence itself; it does not send the sequence header or documentation. Use the command-line parameter -CARriage to have carriage-return characters inserted at a user-defined interval.

EXAMPLE

[ Previous | Top | Next ]

To send the sequence in the file zein.seq to a waiting microcomputer:


% spew

  SPEW out what sequence file ?  zein.seq

  Type a <Ctrl>F now

TCGCACATATTATTGAGACCAACTAGCAACATAGAAAGCACAATATTGTA...

%

OUTPUT

[ Previous | Top | Next ]

When you type <Ctrl>F, the sequence in zein.seq is displayed on your terminal.

INPUT FILES

[ Previous | Top | Next ]

Spew accepts a single nucleotide or protein sequence as input.

RELATED PROGRAMS

[ Previous | Top | Next ]

GetSeq sends sequences from a microcomputer terminal to the computer that runs the Wisconsin Package(TM).

RESTRICTIONS

[ Previous | Top | Next ]

The sequence is transferred without any carriage control and completely without documentation, numbering, or comments.

When the transfer is complete, the program sends a carriage return and a % prompt to the terminal. If you want, you can also have some end-of-transfer character sent.

DEVICES REQUIRED

[ Previous | Top | Next ]

A microcomputer running communications software that can receive files with no carriage control is all that you need.

COMMAND-LINE SUMMARY

[ Previous | Top | Next ]

All parameters for this program may be added to the command line. Use -CHEck to view the summary below and to specify parameters before the program executes. In the summary below, the capitalized letters in the parameter names are the letters that you must type in order to use the parameter. Square brackets ([ and ]) enclose parameter values that are optional. For more information, see "Using Program Parameters" in Chapter 3, Using Programs in the User's Guide.


Minimal Syntax: % spew [-INfile=]zein.seq -Default

Prompted Parameters:

Ctrl-F        starts the transmission

Local Data Files:  None

Optional Parameters:

-STARtchar=4   sets <Ctrl>F to be the character that starts transmission
-ENDchar=4     puts <Ctrl>D at the end of the transmission
-WAIt=1.0      waits one second after the transmission
-CARriage=50   puts a carriage return and line feed every 50 characters

LOCAL DATA FILES

[ Previous | Top | Next ]

None.

PARAMETER REFERENCE

[ Previous | Top | Next ]

You can set the parameters listed below from the command line. For more information, see "Using Program Parameters" in Chapter 3, Using Programs in the User's Guide.

-STArtchar=6

By default, the program sends the sequence after you type <Ctrl>F. Use the -STArtchar parameter to change this behavior. The -STArtchar value is the decimal value of the ASCII character you want to type before transmission. The number may not be 3 since that character (<Ctrl>C) is the program interrupt character on UNIX.

-ENDchar=4

Usually, the program sends no character to imply end of transmission. If you use this parameter, it sends a character, <Ctrl>D (or ^D) in this example, at the end of the transmission. The -ENDchar value is the decimal value of the ASCII character to be sent. If a waiting period is used, the end-of-transmission character is sent before the waiting period begins. If carriage control is used, the end-of-transmission character is sent as the only character on the last record.

-WAIt=1.0

Usually, the program does not wait at the end of transmission. This parameter lets you set a waiting period of up to 15 seconds after transmission is complete. The number (1.0, in this case) is the number of seconds to wait after the sequence is completely sent.

-CARriage=50

inserts a carriage return and line feed every 50 characters. If you use carriage control, the carriage returns cannot be more than 512 sequence characters apart. The carriage control comes before the end-of-transmission character, if one is used.

Printed: December 9, 1998 16:27 (1162)

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


Documentation Comments: doc-comments@gcg.com
Technical Support: help@gcg.com

Copyright (c) 1982-2001 Genetics Computer Group, Inc. A subsidiary of Pharmacopeia, Inc. All rights reserved.

Licenses and Trademarks Wisconsin Package is a trademark of Genetics Computer Group, Inc. GCG and the GCG logo are registered trademarks of Genetics Computer Group, Inc.

All other product names mentioned in this documentation may be trademarks, and if so, are trademarks or registered trademarks of their respective holders and are used in this documentation for identification purposes only.

Genetics Computer Group

www.gcg.com