Topirall

• TOPIRALL
  • FUNCTION
  • DESCRIPTION
  • AUTHOR
  • EXAMPLE
  • OUTPUT
  • INPUT FILE
  • COMMAND-LINE SUMMARY
  • LOCAL DATA FILES
  • OPTIONAL PARAMETERS
    • -LEFt
    • -RIGht

TOPIRALL

FUNCTION

ToPirAll is a utility program that converts a list of sequences, or ranges of sequences, into PIR format for use in other non-GCG programs, especially CLUSTALV.

DESCRIPTION

ToPirAll reads a file of sequence names, with optional ranges specified on each line, and writes a single output file in PIR format.

AUTHOR

This program was written by 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 sample session with ToPirAll

  
  
  % topirall
  
   TOPIRALL of what input file(s) : hth.fil
  
   What should I call the output file (* hth.pir *) ?
  
  %
  

OUTPUT

The output from ToPirAll is a set of sequences in a single files in PIR format.

INPUT FILE

The input file for ToPirAll is a GCG file of sequence names, with the option to include qualifiers -BEGin -END and -REVerse on each line.

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: % topirall [-INfile=]hth.fil -Default
  
  Prompted Parameters:
  [-OUTfile=]hth.pir        Output file
  
  Optional Parameters:
  
  -LEFt=0                   Left margin for sequence in output file
  -RIGht=70                 Right margin for sequence in output file
  

LOCAL DATA FILES

None.

OPTIONAL PARAMETERS

The parameters and switches listed below can be set from the command line. For more information, see "Using Program Parameters" in Chapter 3, Basic Concepts: Using Programs in the GCG User's Guide.

-LEFt=0

sets the left margin for the sequence in the output file.

-RIGht=70

sets the right margin for the sequence in the output file.

Printed: April 22, 1996 15:56 (1162)