encode.py

Numerically encode sequences in a fasta file.

-out           name of outfile
-enc           { [aa] | none | nucl | anucl | cvg | oz | desc
               } Encoding type
    aa             default neunet aa encoding
    none           just print unmodified tab-delimited sequence characters
                   
    nucl           nucleotides without ambiguties
    anucl          nucleotides with ambiguties
    cvg            coverage: gaps get 0's
    oz             consensus characters are 0, other are 1 (CANNOT
                   be used with -degap option)
    desc           numbers most common character 1 next most common
                   2, etc (CANNOT be used with -degap option)
-degap         remove gap characters from sequences
-v             { [0] } verbosity
-h             help
-delim         { [tab] } delimiter character for output table
-debug         { [interleave] } provides some debugging options
-version       print version info and exit

$Id: encode.py,v 1.1 2004/10/10 02:53:10 nghoffma Exp $