Ig2nbrf

• IG2NBRF
  • FUNCTION
  • DESCRIPTION
  • AUTHOR
  • EXAMPLE
  • OUTPUT
  • INPUT FILE
  • COMMAND-LINE SUMMARY

IG2NBRF

FUNCTION

Ig2Nbrf is a utility program that converts an IG formatted file into an NBRF formatted database which PirToGcg can index.

DESCRIPTION

Ig2Nbrf reads a database file in IntelliGenetics format, and writes three NBRF format database files. Two of these, with the extensions ".ref" and ".seq", can be indexed with GCG's PirToGcg utility to make a database in GCG format. The third, with the extension ".ttl", is used by NBRF database programs.

Ig2Nbrf is a simple utility program, without the normal EGCG command line processing. he input filename and the base name for the output database must be provided on the command line.

The original use for the program was to reformat the IG format version of J. Jurka's HUMREP database (file "humrep.dat". The sequences in this file should end with a "1". Where the "1" is missing, Ig2Nbrf "autosaves" the sequence and reports this to the user.

AUTHOR

This program was written by Jack Leunissen (E-mail: jackl@caos.kun.nl Post: CAOS/CAMM Center, University of Nijmegen, Toernooiveld 1, 6525 ED Nijmegen, The Netherlands).

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 @Name@ .

  
  
  % ig2nbrf repbase.dat humrep
  AUTOSAVED MER7
  AUTOSAVED MER24
  AUTOSAVED IVR
  %
  

OUTPUT

The output from Ig2Nbrf is a set of three database files in NBRF foprmat.

INPUT FILE

The input file for Ig2Nbrf is an IG format sequence file.

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: % ig2nbrf database.ig newdbname
  
  Prompted Parameters: None
  
  Local Data Files: None
  
  Optional Parameters: None
  
  
  

Printed: April 22, 1996 15:53 (1162)