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The scanps_defaults.dat file

The scanps_defaults.dat contains settings for valid commands. When you first install scanps, you will have to modify this file to define the correct locations for your directories. For example:

DB_DIR      /gjb/delly/databases/scanps/
MATRIX_DIR  /gjb/delly/gjb/c/scanps/gjscanps/mat/ 
GENERAL_DIR /gjb/delly/gjb/c/scanps/gjscanps/dat/
MATRIX_FILE PAM250
MAX_NSEQ 5000000
CODON_FILE codon.dat
MATRIX_FILE nmd.mat
MAX_NSEQ 500000
MAX_SEQ_LEN 400000
LD_PEN 1 
LI_PEN 8
DB_FORMAT 0

This defines the directories for various files. See the specific command summary below for further details.

Commands in the scanps_defaults.dat file may either be the full command name or an alias as defined in the scanps_alias.dat file (see below). Usually, it is best to use the full command name in the scanps_defaults.dat file. Aliases are there to ease typing commands on the command line. Note that ALL commands and their aliases are case sensitive.



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Geoff Barton (GJB) 2002-07-23