GETSEQ

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

FUNCTION

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GetSeq reads a sequence from a computer that is acting as a terminal and writes it into a new sequence file in GCG format on the computer running the Wisconsin Package.

DESCRIPTION

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GetSeq offers you a quick way to create a GCG sequence file from the keyboard without having having to use SeqEd, Reformat, or a text editor. In addition, if you use a microcomputer that can act as a terminal, you can use GetSeq to move sequence files in text format from your microcomputer into your UNIX directory in GCG format. The microcomputer's terminal emulation software must be able to send ASCII text files to the Wisconsin Package(TM) program GetSeq.

When you run GetSeq, it opens a file that you name and then waits for input. You can either type the sequence characters in from the keyboard, or use your microcomputer's terminal emulation software to send a text file that contains sequence data.

GetSeq accepts all of the supported GCG sequence characters you send until it sees a <Ctrl>D. Then it writes those characters out as a sequence file that can be used by any GCG program. Since GetSeq only accepts sequence characters (see Appendix III), the sequence may be in any format; line feeds, carriage returns, spaces, and numbering are ignored. If you are sending a sequence text file to GetSeq, make sure it doesn't contain comments. Any letters in a comment that are valid sequence symbols will be treated as sequence data.

EXAMPLE

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Here is a session using GetSeq; the sequence GATTCCGATTG was sent followed by <Ctrl>D:


% getseq

  GETSEQ into what sequence file ?  temp.seq

  Now start the sequence transfer . . .
  End the transfer with a <Ctrl>D

   GATTCCGATT G^D

  Bases transferred: 11

%

OUTPUT

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Here is the output file:


!!NA_SEQUENCE 1.0
 GETSEQ from Edelman, October 20, 1996 10:13.

       Length: 11  September 29, 1998 18:05  Type: N  Check: 4920  ..

       1  GATTCCGATT G

RELATED PROGRAMS

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The UNIX % cat > temp.txt command creates a regular text file and puts all of the characters you send from the terminal into it until you send a <Ctrl>D. (Typing <Return> starts a new record in the file -- it does not terminate text entry.)

Reformat is a utility for changing a text file that contains a sequence into a GCG sequence file.

SeqEd lets you edit a sequence and the documentary heading once you have the sequence as a file in GCG format.

RESTRICTIONS

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Your sequence must use the IUB-IUPAC character set for protein or nucleic acid sequences (see Appendix III). Change the sequence with a text editor on the micro if there are any characters in it that are unacceptable to the Wisconsin Package.

The sequence must not be longer than 350,000 characters to be acceptable to Wisconsin Package software.

If there is non-sequence data in the file, such as heading or documentary information, you must have a way to send only the sequence characters. You may need to edit the file on the microcomputer to remove non-sequence sections from the file.

SEQUENCE TYPE

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When GetSeq writes GCG sequence files, it assigns the sequence type based on the composition of the sequence characters. This method is not fool-proof, so you may need to change the sequence type of the newly created file. Look on the last line of the text heading just above the sequence itself for Type: N or Type: P. If the type is incorrect, see Appendix VI for information on how to change or set the type of a sequence.

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 16:27 (1162)

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


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