translate.py

Translates a fasta format file containing nucleotide sequences. Can filter 
translated sequences according to length, presence of unwanted characters
(like X,*).

-degap         Gap characters (-.~) are removed as file is read.
-filter        looks for a filterfile (-filter=filterfile) with
               instructions for rejection of sequences. Filterfile
               is of format: [character to find][max number of
               occurrences to allow]
Example:
if the filterfile looks like:
* 0
X 2
Sequences with > 0 *'s or > 2 X's will be rejected.

-maxlen        { [100000] } Reject translated sequences less than
               this length. Will apply to the length of the degapped
               sequence if -degap is selected.
-minlen        { [0] } Set minimum length of translated sequence.
-f             { [1] } frame; specify reading frame 1, 2, or 3
-out           Name of outfile.
-amb           { [ambi] | unambi } Ambiguity handling
    ambi           codons containing IUPAC ambiguity characters will
                   be translated if a unique amino acid is encoded.
                   
    unambi         causes any codon containing an ambiguity to be
                   translated as an 'X'.
-h             Print documentation.
-v             { [1] } verbosity; 0 for no output.
-version       print version info and exit

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