descEncode (
        seq,
        table,
        startat=0,
        )

seq sequence object table list of dictionaries from SeqIO.tabulate returns a list of ints

main ()

%(filename)s

Numerically encode sequences in a fasta file.

{{out name of outfile}} {{enc 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 verbosity 0}} {{h help}} {{delim delimiter character for output table tab}} {{debug provides some debugging options interleave}} {{version print version info and exit}}

%(version)s

makeDescDict ( dictIn,  start )

dictIn is dictionary defining aa composition at a single position as defined by SeqIO.tabulate

Encodes most abundant char as startat, next most abundant as startat + 1 , etc ties are broken by assigning char lower in alphabet the higher value

returns a new dict

ozEncode (
        seq,
        table,
        cons=0,
        noncons=1,
        )

Encodes consensus and noncons chars as specified seq sequence object table list of dictionaries from SeqIO.tabulate returns a list of ints