Egetseq

• EGETSEQ
  • FUNCTION
  • DESCRIPTION
  • AUTHOR
  • EXAMPLE
  • OUTPUT
  • RELATED PROGRAMS
  • RESTRICTIONS
  • SEQUENCE TYPE
  • COMMAND-LINE SUMMARY
  • LOCAL DATA FILES
  • OPTIONAL PARAMETERS

EGETSEQ

FUNCTION

EGetSeq 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. EGetSeq is a version of GCG's GetSeq with command line control.

DESCRIPTION

EGetSeq 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 EGetSeq 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 EGetSeq

When you run EGetSeq 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.

EGetSeq accepts all of the supported GCG sequence characters you send until it sees a D. Then it writes those characters out as a sequence file that can be used by any GCG program. Since EGetSeq 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 EGetSeq make sure it doesn't contain comments. Any letters in a comment that are valid sequence symbols will be treated as sequence data.

AUTHOR

This GCG program was modified by Jaakko Hattula (Tampere University of Technology, Finland) and Peter Rice (E-mail: pmr@sanger.ac.uk Post: Informatics Division, The Sanger Centre, Hinxton Hall, Cambridge, CB10 1RQ, UK).

All EGCG programs are supported by the EGCG Support Team, who can be contacted by E-mail (egcg@embnet.org).

EXAMPLE

Here is a session using EGetSeq the sequence GATTCCGATTG was sent followed by D:

  
  
  % egetseq
  
    EGETSEQ into what sequence file ?  temp.seq
  
    Now start the sequence transfer . . .
    End the transfer with a D
  
GATTCCGATT G^D
  
    Bases transferred: 11
  
  %
  

OUTPUT

Here is the output file:

  
  
   EGETSEQ from olson, August 12, 1994 10:31.
  
    Length: 11  August 12, 1994 10:31  Type: N  Check: 4920  ..
  
    1  GATTCCGATT G
  
  

RELATED PROGRAMS

GetText reads a text file from a computer that is acting as a terminal and writes a new text file with the same contents and format on the computer running the Wisconsin Package.

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 D. (Typing 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

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

When EGetSeq 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

All parameters for this program may be put on the command line. Use the option -CHEck to see the summary below and to have a chance to add things to the command line before the program executes. In the summary below, the capitalized letters in the qualifier names are the letters that you must type in order to use the parameter. Square brackets ([ and ]) enclose qualifiers or parameter values that are optional. For more information, see "Using Program Parameters" in Chapter 3, Basic Concepts: Using Programs in the GCG User's Guide.

  
  
  Minimum Syntax: % egetseq [-OUTfile=]new.seq -Default
  
  Prompted Parameters: None
  
  Local Data Files: None
  
  Optional Parameters: None
  
  

LOCAL DATA FILES

None.

OPTIONAL PARAMETERS

None.

Printed: April 22, 1996 15:52 (1162)