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File names

File names in the scanps_defaults.dat file MUST NOT be fully qualified. Thus,


will look in the users' current directory for the file. If the matrix file was in /data/local/scanps/matrices you would have to define:

MATRIX_DIR /data/local/scanps/matrices/

as well.

This is also true of the binary database files. The directory for these may be defined by DB_DIR. e.g.

DB_DIR /data/local/databases/scanps/
BDB_ROOT pir66

would look for the files pir66.bix and pir66.bsq in the directory /data/local/databases/scanps.

The only other directory that can be specified in this way is GENERAL_DIR, this holds "other" files needed by the program. At the moment, the only file that is put in GENERAL_DIR is the CODON_FILE for use with DNA vs protein comparisons. More of that later...

Geoff Barton (GJB) 2002-07-23